First thing to try is to move all *.cnm files out of your mailbox directory (.cnm files are messages in your New Mail folder, one per message). Test Pegasus Mail. If no crash then you need to isolate the problem .cnm file (if the crash still occurs, skip the rest of the paragraph). First look for any with 0 byte size. If you find any, there is a pretty good chance they are causing the problem so move the others back into the mailbox directory and test. If you still crash then move them all back out and move a small number back at a time testing between batches until the crash occurs. Now work with that batch to isolate the problem file. This is a trial and error process which can be tedious if you keep a lot of message in the new mail folder. It will be easier to isolate a problem file if you empty the new mail folder between batches by moving the messages to a different Pegasus Mail folder after each successful test.
If moving of the .cnm files did not resolve the crash problem then look at the date stamp of a file named HIERARCH.PM located in the mailbox directory and see if it was last modified around the time that problem started occurring. If so, it is possible that the HIERARCH.PM file has become corrupted. Fixing this requires restoring from a backup (which in your case would need to be from before the problem started occurring) or rebuilding the HIERARCH.PM file. In either case the first step is to get the existing copy out of the way. With Pegasus Mail closed, rename the existing HIERARCH.PM file to something like HIERARCH_PM.BAD.
Restore HIERARCH.PM from a backup if you are so
lucky as to have one from before the problem started occurring. If that is not an option, Pegasus Mail will rebuild the HIERARCH.PM file automatically the next time it starts. Be advised that a rebuild of the HIERARCH file will result in the loss of any filing tray structure you had in your folder list. All folders in the Pegasus Mail folder list will be at the root level.
If you do not know where your mailbox directory is located, open Pegasus Mail and click the Info button located in the Help > About Pegasus Mail... screen. Look for the "Home mailbox location" entry.
Also, in the Announcement and FAQS section of this forum is a post titled "How to deal with crashes and hangs/freezes" which you might find useful.