In an instance of Pegasus Mail that I run off a USB stick I was no longer able to save messages to the copies to self folder. The process acted normally but the copies to self folder always showed a zero message count and opened empty. A restart did not help nor did a reindex. Hierarch looked fine as well. I could find no explanation or solution so decided I would replace the copies to self folder with the default one. When I deleted the copies to self folder from within Pegasus Mail it did not disappear as expected but instead changed to displaying the message count. It now opens with messages, including the ones that I thought were not being saved. New saves now work as they should.
I have compared the file list in the current mailbox directory to a recent backup and they are the same. I would like to understand what happened as it might help someone else who is experiencing issues with copies to self so would appreciate feedback from anyone with any ideas.