A clean-up of the server mailbox before attempting to download is a good approach if web access isn't so cludgy as to make that impractical.  Beyond that. I think you approach is the best you can hope for. 

As for upgrading, it won't fix any existing problems.  They're almost always associated with configuration files which an upgrade won't touch other than to add entries it needs.  The only real way to clean house is to do a clean install including creating new mailboxes and then copying the data over from the previous mailboxes.

BTW, there is a file maintained by Pegasus Mail that keeps track of the messages downloaded.  When it gets corrupted, Pegasus Mail downloads all message again if you've left them on the server.  This happens occasionally on my flash drive installed pmail and I don't know why.  I now routinely web access the server and clean out the new mail.

 I have something under three thousand total messages on the local server, some going back 10-12 years. I already had my earliest messages on Pegasus (V-4.63, win32) but have recently been trying to download more of the  old messages, with difficulty.  I am using POP3 on a slow landline and am having two problems. First, most times the Selective Download has quit after reaching something over 2000 message headers, according to the status message on the bottom left. Because a new folder apparently isn't produced until the process finishes, the work seems all lost. Last time, I was able to preserve the error message and copy the trace, but the information means nothing to me. It's available if of use to any helper.
My first  questions  are:
1). Why is the likely cause of the error, and can I do anything to lessen it? The receiving Timeout is set to 90 seconds.
2). After stopping due to such an error, does a temporary file still exist and if so, how can I access it to continue the message download process? The header download itself takes, I'd guess, about 40 minutes to complete.

Next, when I successfully got the list and proceeded (after going through Internet Options to set  the Download tab at 200 messages), only 20 messages actually were processed, even though many more were marked. Can someone explain what happened here and if I should check for or change some setting? I have reset the tab to 999 in case the last digit isn't actually read.
Should it be possible using POP3 to send from one or more of my Yahoo alias addresses (see below for explanation of these)? Years ago, when I tried to configure for this, it seemed that different User settings all applied to my main address only, and I saw no other means (unless perhaps having different Users on the computer, each with a different Pegasus program installed?).

Lastly, I understand using IMAP is faster and allows seeing other folders (Sent, Trash, and any others) still on the server. I have been told such data is only shown, not actually downloaded (as when using POP3), but that it should include sent alias messages too.  
Can someone point me towards anything which explains in greater detail than the Help section, the entire working of the system when using IMAP? I'm often tired and slow and really would appreciate having  things explained in greater detail than I see there.  Internet searches I've done so far haven't provided the results I'm interested in.

Here is more information explaining my situation:

As most people know, about a year ago Yahoo was sold to Verizon which has combined it and AOL into a new company registered in Ireland. Last week, my computer screen showing Yahoo Mail suddenly, with no prewarning,  switched to another page, with new TOS and an acceptance box. The new terms are unacceptable to me (see the following):
http://newyork.cbslocal.com/2018/04/19/yahoo-aol-read-email-privacy/
and I haven't checked my new (but infrequent) mail since then. Although few of my old messages are important, some are useful for reference so worth keeping.

When I first got on a computer a dozen years ago, I was introduced to Pegasus by a New Zealand acquaintance. I used it for quite a while but eventually also began using a local company, Yahoo, which was provided by my phone service. My main address was (name)@sbcglobal.net but Yahoo also provided multiple 'disposable' addresses of the form (alias-[xxx])@yahoo.com where [xxx] could be varying words or numbers, giving the multiple entities. These aliases were used with/for different associations and purposes, thus safeguarding my main address, allowing automatic sorting, and helping identify Spam. Pegasus could receive return messages with these addresses, but I couldn't find a way to send from them using Pegasus so I mostly used Yahoo after that time.
My first computer started acting up about five years ago so I saved all my Pegasus files elsewhere. After reinstalling  all of them on a new system, none of the old messages on the server were recognized as already downloaded, and Peg. tried to download new copies, starting with the earliest of the messages. I had an even slower connection then and was unable to Selectively Download because the connection invariably failed before the whole list was gotten, so I gave up using it to retrieve new mail, instead keeping old important (or new, copied) mail there.

Thanks for any assistance.

In order to prevent all the delays by forwarding all these messages, I would suggest you use NotSplit extension to extract messages from folders, and then collect them up on a memory stick, or an external disk drive. You can then transfer them to the new copy of Pegasus Mail into its Newmail directory, and then onwards to an appropriate folder. 

Notsplit can be found at the community website.

 Martin

Thanks for the quick reply, but I think you misread my problem. I am trying to download to Pegasus, from the AT&T server, messages I could until recently read using Yahoo Mail, and which aren't anywhere on my machine yet. I was trying to avoid using another program like Thunderbird to access them. Your extension sounds interesting, but I don't understand how it helps my current problem.

I tried the Selective Download again, and  the process stopped at 2417 headers this time; the last time it reached 2599. I may need to try again late tonight, well after midnight, when traffic locally may be less.

What is the ultimate goal?  I sense that you want to download all of the messages which is contrary to the selective download approach.

In your original post you asked about IMAP.  As you already know, the POP3 protocol is used to retrieve messages from a server, optionally leaving them on the server or deleting them from the server once downloaded.  IMAP is a protocol that lets you access the messages on the server.  It's valuable when you need to access the same message store from multiple devices.  Storing messages locally requires that you copy or move messages to a local folder.  Picture your Pegasus Mail folder list containing a second mailbox.  One is what you see now as My mailbox.  They are the local folders.  The other would be a display of the server mailbox folders being accessed via IMAP.

Sorry I missed your point of wanting to download into Pegasus Mail. I would suggest you contact the ISP and ask if they can supply you with a backup copy of your data.

 Martin

[quote user="irelam"]

Sorry I missed your point of wanting to download into Pegasus Mail. I would suggest you contact the ISP and ask if they can supply you with a backup copy of your data.

 Martin

[/quote]

Does that mean you don't know any of the answers to my original questions? I may look into your last suggestion, but still would like to know the answers, even if the latter somehow works.

Might somebody else have any ideas about my problem?

I thought I had posted a reply last night but it hasn't shown up.  Could be that I never hit the Post button or maybe it's held up by a moderator.  Regardless, here goes again.

What is your ultimate goal?  I sense that you want to download all of the messages but the use of selective download is contrary to that.

Changing the subject to your original post about IMAP & POP3, the POP3 protocol downloads mail from a host server whereas the IMAP protocol allows you to work with mail directly on the host server.  The value of IMAP is that you can work with the same mailstore from different devices.  When using IMAP you can download messages for local storage but the process involves copying or moving messages from an IMAP folder to a local folder (Picture having two mailboxes in your folder list.  The existing "My mailbox" one contains your local folders, the one connected via IMAP displays the server ones.  You can copy/move messages between the two as desired).

Yes, your earlier post hadn't shown up last night. [This was posted last night but didn't appear for a while, either.]

Regarding my objective, I wanted to download most, but not all the old mail I didn't already have. I also wanted to understand why, for example, my inbox received some messages sent to some of my Yahoo aliases rather than to my main address.

Selective download brings just headers, so should have less chance of being interrupted before finishing a large list, compared to downloading all complete messages. In both cases, all progress seems to be lost if the process doesn't finish. Also, with Selective, some of the old ones can be marked for deletion rather than deleting after I get them. With Yahoo, I didn't always get around to deleting unneeded messages, plus the need may have dissipated over the years.

Anyway, I continued to try both regular and selective downloads, and seem to have finally gotten most, if not all, my mail. Strange things are happening though; if I start either type of download again, it indicates it's downloading, beginning with message #1 of 2787 or whatever,  then the everything seems to hang up for a while. Afterwards, the stored message count remains the same, implying nothing new was detected/recovered. Seems to me it used to say it was checking, then switch to downloading only newest messages, not all. If so, something in my system may be corrupted and I probably should update to V4.72 to see if that cures it.  Should do update anyway, I suppose. My System Messages include two about Spam; "Spamhalter can't find spam folder", and "Spamhalter message size limit is 250000 bytes"; plus a few POP3 errors, one about downloading, etc.  Shouldn't be any spam on the server; I don't get much but in the past have identified and deleted it without opening, using Yahoo's "Raw View" to see headers.

I may install Pegasus on a stick drive and configure that one for IMAP and if I find messages I need in folders, copy them elsewhere on the drive and also to my backup HDD.