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
100% my own fault, leaving my comment here for anyone experiencing the same thing, but removing the mention of "bug" as this was absolutely not your fault, incredible mod!!
I had a game that bugged and followed some steps online that solved the issue, but had me tempering with my token and persistent file in AppData Roaming. This made the achievement not save properly to the persistent file, thank you for mentioning it!
Solution for other dumb dumbs like me:
- Go to User > AppData > Roaming > RenPy
- delete your Persistent folder (make a copy if you want - i have only a handful of RenPy games, I didn't)
- delete your Token folder (same)
- Restart the game and enjoy!
