A couple things
Just did a quick check using MBXMAINT.EXE and MBXMAINT_UI.EXE.
Located in PMAIL/Programs Directory.

Pegasus uses a similar folder structure to MBOX, not sure how different.
I copied one of my folder pairs EBAY.PMM and EBAY.PMI to another directory.
Ran
MBXMAINT.EXE -CH EBAY.PMM

Got
Pegasus Mail/Mercury mailbox maintenance commandline utility
Copyright (c) 1990-2011, David Harris, all rights reserved.
Checking 'EBAY.PMM'...
Folder appears OK - no consistency errors encountered.

Program is old 2011, but seems to still be valid.
Pegasus Mail/Mercury mailbox maintenance commandline utility
Copyright (c) 1990-2011, David Harris, all rights reserved.

Commandline usage -

MBXMAINT <command_filename> | <option [option...]>

  -QU[IET]
  -CH[ECK] <folder_pmm_path_with_optional_wildcards>
  -CO[MPRESS] <folder_pmm_path_with_optional_wildcards>
  -MO[VE] <source_path> <dest_path>
  -RE[PAIR] <folder_pmm_path>
  -FI[XIDS] <folder_pmm_path>

Did a test on all my folders (PMM files) and it flagged a small number with ID issues.
Ran the -FI option on them, and it did repair, so all are clean now? Only says and issue if using IMAP, which I have never used, but figured better to fix issue.

There is the the UI version of program, but would be a lot more work.
Says it works with wildcards, but didn't seem to do for me. Using wildcards only got 1 folder.
Used (Linux) for a in *.PMM; do ../Programs/MBXMAINT.EXE -CH $a; done >>/tmp/MBXCHECK
Then checked MBXCHECK to see what folders had issues, and run -FI on all of them.

Would be interesting to see if you PMM and PMI files have any issues?
But those are Programs Mr. Harris includes to check folders.

Thx for trying Brian, but I am afraid to touch anything for fear of losing my New Mail folder and my Copies to Self. I was told I have a POP account which I think does not leave any messages on the primary company servor, but are only stored on my hard drive? Or were stored before lost. I suspect I still have them, but they are hidden.

I hope that early on you had made a safety (backup) copy of your mailbox directory. If not, that is the best and easiest way to preserver what you have.

As for POP3 and the host server, POP3 can be configured to either delete or leave mail on the the server. If you don't know how yours is configured, this is how to check:

• Go to Tools > Internet options
• Open the Receiving(POP3) tab
• Select the POP3 host then click the Edit button
• Down near the bottom of that Settings window look for the option "Delete mail from host once it has been successfully retrieved". If it is not checked then Pegasus Mail will not be deleting it as part of its POP3 retrieval process.

The Pegasus Mail folder list is self-repairing, polling the folder files that exist in the mailbox directory each time Pegasus Mail starts up. A folder might only go missing from the Folder list when a duplicate folder name or internal ID is encountered.

What concerns me is the deletion of two folders you mentioned in your original post, and the subsequent discovery of two .PMI files in the mailbox directory that don't have a matching .PMM file. The .PMM files hold mail data. With two missing, I immediately started thinking 'file recovery' which is why I suggested the path of figuring out what is stored in Carbonite that is not in the mailbox directory.

Brian,

I keep trying. Since I am only missing Email that was read and sent to a Folder, ten years worth, I am looking in Admin for any large .pmm files. I found 3 big ones, and I found their matching .pmi files. I even reindexed each folder...still missing....how to I copy my Pmail/Admin files to show here? I open file explorer, go to correct folder, select all, and copy, but it wont paste here?

You would have to redirect a directory listing to a text file or use a third party utility, neither of which are for the novice PC user. Besides, I truly do not believe that would help. Do this and report back:

• Count the number of folders listed in the Pegasus Mail Folder list, excluding "New Mail", "Deleted Messages", and "Recent search results" (the later two may not exist).
• Using a file explorer, count the number of .PMM files in the mailbox directory.
• Using a file explorer, count the number of .PMI files in the mailbox directory.

If you are comfortable using Find in a file explorer then a search for .PMM and then one for .PMI could be the easiest way to get those counts.

Hope you can handle opening a cmd prompt
cmd

That should open a terminal window.

Change to the PMAIL MAIL folder
usuall would be C:\PMAIL\MAIL
do a dir
If it shows .PMM and PMI files you have a singlue user set.
If it only shows PMAIL.USR and subdirectories, it is a multi-user setup.
May just have ADMIN subdirectory, but could have others
If it has just ADMIN change to it.
cd ADMIN
Then do the following command to see directories.
dir .PMM .PMI*
That would show files with PMM or PMI in them, since you said you renamed some to .old

To redirect that information to a text files could do something like this.

dir .PMM .PMI >LIST_OF_PMM_AND PMI.txt

That would create a file LIST_OF_PMM_AND PMI.txt that would contain the listing.

wrote a program testhier.cpp long ago. Don't recall why?
It looks at the
HIERARCH.PM File to examine folders and trays.
So, probable would work with you file, might be ok with ok with a backed up copy of files.

Mail Folder
"024B349:My mailbox"

Trays
1,0,"7FE82963:DADTRAY","024B349:My mailbox","DADTRAY"
1,0,"4DB14767:G4LTRAY","024B349:My mailbox","G4LTRAY"
1,0,"08FE2816:COPYTRAY","024B349:My mailbox","COPYTRAY"
1,0,"6FC54766:MAINTRAY","024B349:My mailbox","MAINTRAY"
1,0,"3C8A5551:USPSTRAY","024B349:My mailbox","USPSTRAY"
1,0,"76751789:PMAILTRAY","024B349:My mailbox","PMAILTRAY"
1,0,"12C82225:ElaineTray","024B349:My mailbox","ElaineTray"
1,0,"0F641206:EbayTray","024B349:My mailbox","EbayTray"
1,1,"607E2600:Recent search re","024B349:My mailbox","Recent search results",1,20

Folders in Trays (Not Main Folder)
COPY1314.PMM    Y 0,0,"5OUTNTZZ:5CC5:COPY1314","08FE2816:COPYTRAY","Copy1314"
COPY2000.PMM    Y 0,0,"UAPFMJM3:7A58:COPY2000","08FE2816:COPYTRAY","Copy2000"
COPY2001.PMM    Y 0,0,"NP13X71Y:6176:COPY2001","08FE2816:COPYTRAY","Copy2001"
COPY2002.PMM    Y 0,0,"4EP2LN9Z:6177:COPY2002","08FE2816:COPYTRAY","Copy2002"
COPY2003.PMM    Y 0,0,"CE0LCQIN:6178:COPY2003","08FE2816:COPYTRAY","Copy2003"
COPY2004.PMM    Y 0,0,"RJGEYE3R:6179:COPY2004","08FE2816:COPYTRAY","Copy2004"
COPY2005.PMM    Y 0,0,"ZJRXOHCF:617A:COPY2005","08FE2816:COPYTRAY","Copy2005"
COPY2006.PMM    Y 0,0,"SBFWUL0V:7536:COPY2006","08FE2816:COPYTRAY","Copy2006"
COPY2007.PMM    Y 0,0,"IWHKVB32:6174:COPY2007","08FE2816:COPYTRAY","Copy2007"
COPY2008.PMM    Y 0,0,"AY8RGEMX:6175:COPY2008","08FE2816:COPYTRAY","Copy2008"
COPY2009.PMM    Y 0,0,"C7X7CSP5:23BE:COPY2009","08FE2816:COPYTRAY","Copy2009"
COPY2010.PMM    Y 0,0,"QOOZDVTD:5599:COPY2010","08FE2816:COPYTRAY","Copy2010"
COPY2011.PMM    Y 0,0,"0O3QIVY7:559A:COPY2011","08FE2816:COPYTRAY","Copy2011"
COPY2012.PMM    Y 0,0,"YMOG8BN4:46D0:COPY2012","08FE2816:COPYTRAY","Copy2012"
COPY2015.PMM    Y 0,0,"5MDK54HK:72D0:COPY2015","08FE2816:COPYTRAY","Copy2015"
COPY2016.PMM    Y 0,0,"YXBMYZ2F:72D1:COPY2016","08FE2816:COPYTRAY","Copy2016"
COPY2017.PMM    Y 0,0,"DACD8HA4:72D2:COPY2017","08FE2816:COPYTRAY","Copy2017"
COPY2018.PMM    Y 0,0,"J39XXZ1C:72D3:COPY2018","08FE2816:COPYTRAY","Copy2018"
COPY2019.PMM    Y 0,0,"2CMM31CS:2128:COPY2019","08FE2816:COPYTRAY","COPY2019"
COPY2020.PMM    Y 0,0,"M82PYM4C:2129:COPY2020","08FE2816:COPYTRAY","COPY2020"
COPY2021.PMM    Y 0,0,"2R25QWAB:212A:COPY2021","08FE2816:COPYTRAY","COPY2021"
COPY2022.PMM    Y 0,0,"N1UYU4DT:212B:COPY2022","08FE2816:COPYTRAY","COPY2022"
DAD1.PMM        Y 0,0,"6Z1ADN84:2DB3:DAD1","7FE82963:DADTRAY","DAD1"
DAD2.PMM        Y 0,0,"AAS2Q8AJ:2DB4:DAD2","7FE82963:DADTRAY","DAD2"
EBAYOLD.PMM     Y 0,0,"1R7XUGGN:2C66:EBAYOLD","0F641206:EbayTray","EbayOld"
EBAYOLD2.PMM    Y 0,0,"9PD4GI7C:781A:EBAYOLD2","0F641206:EbayTray","EbayOld2"
ELAINE1.PMM     Y 0,0,"HJA1BB1D:556E:ELAINE1","12C82225:ElaineTray","Elaine1"
ELAINE2.PMM     Y 0,0,"UO9ISKVO:556F:ELAINE2","12C82225:ElaineTray","Elaine2"
ELAINE3.PMM     Y 0,0,"PR4BDCNE:5901:ELAINE3","12C82225:ElaineTray","Elaine3"
G4L0408.PMM     Y 0,0,"3KSSC1HB:6771:G4L0408","4DB14767:G4LTRAY","G4L0408"
G4L0909.PMM     Y 0,0,"83DWN76M:7E6A:G4L0909","4DB14767:G4LTRAY","G4L0909"
G4L1011.PMM     Y 0,0,"3KDTLD71:6772:G4L1011","4DB14767:G4LTRAY","G4L1011"
G4L1213.PMM     Y 0,0,"7Z6IHUB1:6773:G4L1213","4DB14767:G4LTRAY","G4L1213"
G4L1418.PMM     Y 0,0,"3H0Q9YJ9:042F:G4L1418","4DB14767:G4LTRAY","G4L1418"
G4L1920.PMM     Y 0,0,"RZOHOY4Q:2A8B:G4L1920","4DB14767:G4LTRAY","G4L1920"
G4L2122.PMM     Y 0,0,"3OOSMBJP:2E68:G4L2122","4DB14767:G4LTRAY","G4L2122"
G4L2324.PMM     Y 0,0,"URAJ5V4B:59AE:G4L2324","4DB14767:G4LTRAY","G4l2324"
MAIN2003.PMM    Y 0,0,"DJHBYUKV:5478:MAIN2003","6FC54766:MAINTRAY","Main2003"
MAIN2004.PMM    Y 0,0,"DVM87FYO:5479:MAIN2004","6FC54766:MAINTRAY","Main2004"
MAIN2005.PMM    Y 0,0,"60TOHB32:4255:MAIN2005","6FC54766:MAINTRAY","Main2005"
MAIN2006.PMM    Y 0,0,"5Y00PGC7:5D6D:MAIN2006","6FC54766:MAINTRAY","Main2006"
MAIN2007.PMM    Y 0,0,"E5JG7AV3:5D6E:MAIN2007","6FC54766:MAINTRAY","Main2007"
MAIN2008.PMM    Y 0,0,"ZA2JSAID:3FA2:MAIN2008","6FC54766:MAINTRAY","Main2008"
PMAIL2020.PMM   Y 0,0,"E8OJWE5E:571D:PMAIL2020","76751789:PMAILTRAY","PMAIL2020"
PMAIL2021.PMM   Y 0,0,"EM1LN1WP:571E:PMAIL2021","76751789:PMAILTRAY","PMAIL2021"
PMAIL2022.PMM   Y 0,0,"T7N2J0AW:4D5B:PMAIL2022","76751789:PMAILTRAY","PMAIL2022"
PMAIL2023.PMM   Y 0,0,"3VMJVXZ0:2079:PMAIL2023","76751789:PMAILTRAY","PMAIL2023"
PMAIL2024.PMM   Y 0,0,"MG2ZS3H6:03EA:PMAIL2024","76751789:PMAILTRAY","PMAIL2024"
USPS2018.PMM    Y 0,0,"FUIF553Y:23DE:USPS2018","3C8A5551:USPSTRAY","USPS2018"
USPS2019.PMM    Y 0,0,"8QM3VKXP:3337:USPS2019","3C8A5551:USPSTRAY","USPS2019"
USPS2020.PMM    Y 0,0,"V3VV7J9V:3338:USPS2020","3C8A5551:USPSTRAY","USPS2020"
USPS2021.PMM    Y 0,0,"MRHQQDQ7:3873:USPS2021","3C8A5551:USPSTRAY","USPS2021"
USPS2022.PMM    Y 0,0,"X7FTDG6F:575E:USPS2022","3C8A5551:USPSTRAY","USPS2022"
RECENT SEARCH RE.PMM N 0,0,"46778351d939517ba9f00144c7c7ea76","607E2600:Recent search re","Pet Shippers Guam (7 Sep 25 5:RECENT SEARCH RE.PMM N 02)"
RECENT SEARCH RE.PMM N 0,0,"5afdde9d3df8a43e2028f4f90a6d0de3","607E2600:Recent search re","sleep.conf (5 Oct 25 22:38)"

Folders in Trays in Main Folder
Mailbox/Tray      2,1,"024B349:My mailbox","Michael Setzer II","Michael Setzer II"
1440.PMM        Y 0,0,"Z2OMN80U:25D5:1440","024B349:My mailbox","1440"
ACCOUNT.PMM     Y 0,0,"16D6FBC5:663A:ACCOUNT","024B349:My mailbox","Account"
AFT.PMM         Y 0,0,"5A1ACD52:097A:AFT","024B349:My mailbox","AFT"
ALUMNI.PMM      Y 0,0,"778BEE16:656D:ALUMNI","024B349:My mailbox","Alumni"
AMAZON.PMM      Y 0,0,"3BF8FBD0:663B:AMAZON","024B349:My mailbox","AMAZON"
AMZOLD.PMM      Y 0,0,"O0DY2II5:023F:AMZOLD","024B349:My mailbox","AMZOLD"
ANALOGX.PMM     Y 0,0,"1C84FBD0:663C:ANALOGX","024B349:My mailbox","Analogx"
Mailbox/Tray      1,0,"7FE82963:DADTRAY","024B349:My mailbox","DADTRAY"
Mailbox/Tray      1,0,"4DB14767:G4LTRAY","024B349:My mailbox","G4LTRAY"
BACKUP.PMM      Y 0,0,"67D0FBDF:663F:BACKUP","024B349:My mailbox","Backup"
BILL521.PMM     Y 0,0,"64D8FB72:662F:BILL521","024B349:My mailbox","Bill521"
BLOODBANK.PMM   Y 0,0,"1B9DFC75:6659:BLOODBANK","024B349:My mailbox","Blood Bank"
BOYCOTT.PMM     Y 0,0,"0QB2VFK2:7BE5:BOYCOTT","024B349:My mailbox","Boycott"
BRAIN.PMM       Y 0,0,"01D5FBEC:6641:BRAIN","024B349:My mailbox","Brain Share"
C.PMM           Y 0,0,"AFML8EUK:0F8A:C","024B349:My mailbox","C"
COLLECTZ.PMM    Y 0,0,"069EAFD6:5A1A:COLLECTZ","024B349:My mailbox","CollectZ"
COPYSELF.PMM    Y 0,0,"2BD83F9D:0DF4:COPYSELF","024B349:My mailbox","CopySelf",0,20
CUSTCARE.PMM    Y 0,0,"48F3FCE3:666F:CUSTCARE","024B349:My mailbox","Customer Care"
DAD.PMM         Y 0,0,"184DFC15:6648:DAD","024B349:My mailbox","Dad"
DHARRIS.PMM     Y 0,0,"583E7B7A:113F:DHARRIS","024B349:My mailbox","DHarris"
DISNEY.PMM      Y 0,0,"705FFC25:664B:DISNEY","024B349:My mailbox","Disney"
DONNA_SU.PMM    N 0,0,"0757FB99:6637:DONNA_SU","024B349:My mailbox","DONNA_SUMMERS"
EBAY.PMM        Y 0,0,"69C71ECB:7D08:EBAY","024B349:My mailbox","Ebay"
ELAINE.PMM      Y 0,0,"262EFB99:6638:ELAINE","024B349:My mailbox","Elaine"
FEDORA.PMM      Y 0,0,"0948B824:3D1B:FEDORA","024B349:My mailbox","Fedora"
G4L.PMM         Y 0,0,"DIIIDMTU:0AFD:G4L","024B349:My mailbox","G4L"
G4U.PMM         Y 0,0,"LW7GN12F:31AE:G4U","024B349:My mailbox","G4U"
GFT.PMM         Y 0,0,"1B807959:5B63:GFT","024B349:My mailbox","GFT"
GRC.PMM         Y 0,0,"4060FD28:667D:GRC","024B349:My mailbox","GRC"
GRUB.PMM        Y 0,0,"O2WCFHFD:10C2:GRUB","024B349:My mailbox","Grub"
HARLEY.PMM      Y 0,0,"BF64HBCK:35D9:HARLEY","024B349:My mailbox","Harley"
HERC-XEN.PMM    N 0,0,"2BA4FCC7:6668:HERC-XEN","024B349:My mailbox","Herc-Xena"
IBM.PMM         Y 0,0,"15B7FCBB:6666:IBM","024B349:My mailbox","IBM"
JAY.PMM         Y 0,0,"478E975C:16D1:JAY","024B349:My mailbox","Jay"
JUNK.PMM        Y 0,0,"00C0FD35:667E:JUNK","024B349:My mailbox","Junk or suspicious mail"
KERNEL.PMM      Y 0,0,"C1UU809Q:5FC2:KERNEL","024B349:My mailbox","Kernel"
KEVIN.PMM       Y 0,0,"25EDFD89:668C:KEVIN","024B349:My mailbox","Kevin"
KUENTOS.PMM     Y 0,0,"0D44FCF3:6670:KUENTOS","024B349:My mailbox","Kuentos"
LIBRE.PMM       Y 0,0,"UDCKE6GE:7DD0:LIBRE","024B349:My mailbox","Libre Office"
LINUX.PMM       Y 0,0,"6FB3FD95:668F:LINUX","024B349:My mailbox","Linux"
LYNDAE.PMM      Y 0,0,"556CFDB1:6690:LYNDAE","024B349:My mailbox","LyndaE"
MAIN.PMM        Y 0,0,"0694FC35:664D:MAIN","024B349:My mailbox","Main Folder"
MERCURY.PMM     Y 0,0,"1AD6FCBB:6667:MERCURY","024B349:My mailbox","Mercury"
MOM.PMM         Y 0,0,"12DDFE72:66AE:MOM","024B349:My mailbox","Mom"
MOM-ORG.PMM     Y 0,0,"EC5HSZO9:1BBA:MOM-ORG","024B349:My mailbox","Mom-org"
OPENCOB.PMM     Y 0,0,"Z6A3JHPE:28AA:OPENCOB","024B349:My mailbox","Open Cobol"
OXFORD.PMM      Y 0,0,"WXSNAAA4:005F:OXFORD","024B349:My mailbox","Oxford"
PM-NEWS.PMM     Y 0,0,"264FFDF7:669D:PM-NEWS","024B349:My mailbox","PM-News"
PMAIL.PMM       Y 0,0,"019AFDF7:669C:PMAIL","024B349:My mailbox","Pegasus Mail List"
Mailbox/Tray      1,0,"08FE2816:COPYTRAY","024B349:My mailbox","COPYTRAY"
Mailbox/Tray      1,0,"6FC54766:MAINTRAY","024B349:My mailbox","MAINTRAY"
Mailbox/Tray      1,0,"3C8A5551:USPSTRAY","024B349:My mailbox","USPSTRAY"
REDHAT.PMM      Y 0,0,"2BB74576:0A72:REDHAT","024B349:My mailbox","RedHat"
SALIVE.PMM      Y 0,0,"3TMH6SFS:19C1:SALIVE","024B349:My mailbox","Salive"
SPAM.PMM        Y 0,0,"3B8BA31E:0943:SPAM","024B349:My mailbox","Spam"
SPAMH.PMM       Y 0,0,"IK1H7AZT:54C9:SPAMH","024B349:My mailbox","SpamH"
SQUID.PMM       Y 0,0,"2UE9GFDF:75EF:SQUID","024B349:My mailbox","Squid"
SYSLINUX.PMM    Y 0,0,"BP4JRIND:32D5:SYSLINUX","024B349:My mailbox","Syslinux"
TIGHTVNC.PMM    Y 0,0,"0D5DFB57:1E25:TIGHTVNC","024B349:My mailbox","TightVnc"
TISHAWNNA.PMM   Y 0,0,"ECHSJGQS:3985:TISHAWNNA","024B349:My mailbox","Tishawnna"
Mailbox/Tray      1,0,"76751789:PMAILTRAY","024B349:My mailbox","PMAILTRAY"
USPS.PMM        Y 0,0,"FDI909TU:4AC0:USPS","024B349:My mailbox","USPS"
WATT.PMM        Y 0,0,"5721FE56:66A9:WATT","024B349:My mailbox","Watt"
WEBCAL.PMM      Y 0,0,"5C8F36E1:170C:WEBCAL","024B349:My mailbox","WebCal"
WGET2.PMM       Y 0,0,"ATCPJTA5:36A7:WGET2","024B349:My mailbox","wget2"
ZHAOPEI.PMM     Y 0,0,"25CC2EA6:27EF:ZHAOPEI","024B349:My mailbox","Zhaopei"
Mailbox/Tray      1,0,"12C82225:ElaineTray","024B349:My mailbox","ElaineTray"
Mailbox/Tray      1,0,"0F641206:EbayTray","024B349:My mailbox","EbayTray"
Mailbox/Tray      1,1,"607E2600:Recent search re","024B349:My mailbox","Recent search results",1,20
FOL07A25.PMM    N 0,256,"IXVDUMP3:4575:FOL07A25","024B349:My mailbox","Deleted Messages",0,20
FOL07F06.PMM    N 0,0,"C39E1LEX:1938:FOL07F06","024B349:My mailbox",Name_Unavailable,0,20

Could try these command line options
That would check PMM/PMI pairs for errors.

C:>cd \PMAIL\MAIL\ADMIN
C:\PMAIL\MAIL\ADMIN>....\Programs\MBXMAINT.EXE -CH *.PMM
Pegasus Mail/Mercury mailbox maintenance commandline utility
Copyright (c) 1990-2011, David Harris, all rights reserved.
Checking 'COPYSELF.PMM'...
Folder appears OK - no consistency errors encountered.
Checking 'FOL04182.PMM'...
Folder appears OK - no consistency errors encountered.
Checking 'JUNK.PMM'...
Folder appears OK - no consistency errors encountered.
Checking 'MAIN.PMM'...
Folder appears OK - no consistency errors encountered.

I really appreciate the help, but all this software talk is way beyond me.....here is my Plan. I am going to restore all large matching files, from January 26 the last good day, from my Backup that start with FOL.....pmm or FOL....pmi. Since my missing emails are ten years combined, it has to be a large .pmm file. Here is my question. If Pegasus sees to many .pmm and matching .pmi files, what does it do? How does it chose with pair to display? I might be asking stupid questions.

First, be sure restore the pair (FOL.....pmm and matching FOL.....pmi).

To me, the word "restore" means replacing what is there with what comes from the backup. That is what you want should do, but if you haven't yet captured a copy of your mailbox directory you should do so before you start in order to preserve what is currently there now.

As for "If Pegasus sees to many .pmm and matching .pmi files, what does it do?". I don't know what you mean by "matching" but you must avoid having folder files with the same FOL..... name, hence my comment above to replace. AFAIK, there is no limit to the number of folder files pairs, they just can't be duplicates. After your complete the restore of files but before you start Pegasus Mail, I suggest you rename HIERARCH.PM to HIERARCH.PM_OLD. This will force Pegasus Mail to create a new folder list by polling every .PMM/.PMI file pair in the mailbox directory.