TLDR: Folder window is messed up after a computer crash, a filling tray is gone, and all folders are in the "main branch", the folder for search results is also missing. What can I do?

Backgroud:
I have my copy of Pegasus Mail set up with the Folders window always open, in what I think is called List view (i.e. not Preview). The folder tree has been the same for a very long time, though at times we perhaps add some message folders (to be used with filters), and perhaps also, as I had done, one or several filling trays.

That is, I had the standard message folders and some (but not all, I think, since it now looks completely different post-crash) of the added message folders were organised in a filling tray, say called Miscellaneous.

It looked something like this:
New mail
[Here probably was the system Search folder.]
[Any mail deleted during the session would be here; if none the folder's usually not in the list]
Copy
Diverse/Misc. [Filling tray]
--Several message folders (probably 15-18 )
Junk or suspicious mail
Main folder

And between the "system folders" were probably as mentioned a couple of the message folders that I hadn't moved, years ago, to the filling tray. I think I know which ones.

But when I started PM post a computer crash, has happened before but not with this result in Pegasus Mail, all folders were in alphabetical order, the filling tray gone, and so was the special folder for search results (wasn't in use at this time).

For a split second I first thought I had somehow moved one or two message folders from the filling tray to the "main branch", but realised that they all were there, the filling tray missing, and so was the search folder.

I guess I could simply add a new filling tray, move most of the message folders into it, and be done with it, but I want to know if this can be fixed in some other, proper, way, and what to do with the missing search folder (or will it re-appear if I do a search) etc?

The list displayed in the Folder window is a virtual list. Trays and Folders are not physical locations in the mailbox in the sense of directories and subdirectories. Instead there is a file named HIERARCH.PM that records and maintain the structure of Trays and Folders. When that file gets corrupted, Pegasus Mail will create a new one by polling each of the folder files and adding an entry for each in the new file. The result is the loss of all Tray structure. Recovery of this type of corruption is the restoration of the HIERARCH.PM file from a backup. The backup must be current though. There is not a specific timeframe, my experience of restoration failing due to what I believe is too many differences between the entries in the restored file and the actual folder files that exist. So, the first thing to try is to restore HIERARCH.PM from a recent backup if you have one. Otherwise, your only choice is to manually recreate the Tray structure.

Hint one: To make recovery from a corrupted HIERARCH.PM file easier, for folders within a Tray, include some sort of reference to the parent Tray in the folder name. Example:
Tray = "Invoices"
Folders = "Company1", "Company2", "Company3"
Folder names = "Inv_Company1", "Inv_Company2", "Inv_Company3"

Hint two: Avoid duplicate folder names, even when they are in different Trays. Duplicate names can result in one or all of the duplicate named folders to not appear in the Folder list. The don't get deleted, they just don't get listed. This is an odd one. Duplicate names can exists for years, right up until they don't. I have never been able to identify the trigger that causes this problem but have experienced it a number of times while administering a multi-user installation of Pegasus Mail in a small business (15 users).

Edit: As for the search results folder(s?), a folder named "Recent search results" will be created the next time you do a search. I believe that the results of any previous searches are lost if you can't recover using a restored HIERARCH.PM.

(And also thanks for the hints/info.)

Ah, if we start with the simple things; I did understand that "Deleted" would appear again as soon as something was deleted, but you can confirm that it's the same with Recent search results, good. I've no problems with it being empty, as I said I hadn't used it recently.

Speaking of recent, the sad thing is that I don't have a recent copy of HIERARCH.PM... If I compare the content of a copy of HIERARCH.PM, as it is now, with an old backup, I obviously find the filling tray in the old copy of the file:

1,3,"[removed by me]:My mailbox","Diverse"

But the old version also contains some old entries that seems to point to nowhere, such as:
0,0,"EDSW8N4U:3FA5:FOL008E5","096C883:My mailbox",Name_Unavailable,0,20

There is no such file as "FOL008E5" etc.

And is there any explanation to the "syntax" in HIERARCH.PM, i.e. starting with "2,1" for My mailbox; "1,3" for a filling tray; "0,256" Deleted messages; "1,0" Recent search results; then I have couple of entries (still looking at the old copy of HIERARCH.PM) that start with "2,0" I can't find in the recently recreated HIERARCH.PM. (They are not in alphabetical order in any of the copies of HIERARCH.PM, I assume that is just how PM presents the list in the folder window, but these numbers must have something to do with with the hierarchy and staus of the entries in the list; it being a filling tray etc?)

I know that using PM, in different versions, for very long time, as many tend to do, can result in some old files or entries still being there.

Could restoring an old copy of HIERARCH.PM mess up something, or the contents within the files, say main.PMM, FOLDxyz.PMM etc., i.e. message folders? Guess it's quite easy to test, obviously, if I take a backup of all in PMAIL\MAIL as it is before, then restore/copy the old backup of HIERARCH.PM.

No, but I would have a backup just in case.

Yup. There is no harm in trying this.

Consider adding the -o option to your shortcut command while working through this. This will start Pegasus Mail in offline mode.

Now, where was I, back to business; oh, it's already weekend.

*Guess I also have some housekeeping to do; I'll have to take a look at some of the old files in the mail folder, also see if I can add or remove something in HIERARCH.PM (as well as read the latest about 4.80 and the current beta, since my copy is 4.73; all will be "moved"/installed on a new drive/OS in coming month(s), so guess it's about time). P.S. I had an old account somewhere here, 10-20 year ago, can't remember what I posted, but do remember some exchange, but since then the forum software has changed etc.

If you upgrade, skip 4.80 and go to the 4.81 beta version. It is solid and fixed some bugs that were in 4.80.

Yes, this forum software changed. I don't the exact details was aware of the scramble to recover forum history and then the search for a forum platform onto which it could be transferred.

Before moving to a new drive/OS, consider posting for advice on the best way to go about it. Provide details of what you want to accomplish. Hopefully we can help make it as easy as possible.