I just noticed this today. At first, I assumed it's due to the 1 August 2022 update (1.38.0), but I find that I am still running 1.37.0. Although most of my settings were OK, at least the mapping/syncing of special folders was lost.
The symptom was that messages deleted in Aqua Mail continued to show up as not deleted on other IMAP email clients. I eventually found that the sync settings for the Deleted, Sent, and Draft folders were set to "do not sync". When I changed them to "sync with" the corresponding special folder, the problem was resolved.
Also, Aqua Mail seems to have forgotten the half dozen or so recently used "Other folders". This is not a big deal, but might be a clue about what happened.