Huh, that's weird. Achievements are saved in the persistent file so they should stay unlocked once you got them. Haven't heard about any issues with that from other players.
The only thing that comes to mind is issues with persistent file itself because of Renpy upgrade. There is some code that handles changes for that and maybe it rewrites the achievements in rare cases. You can try deleting your persistent file (after backing it up) to see if it works better with a clean one