So there's no way to anticipate that issue? If you start the game, persistent file is overwritten before you can do anything? Damn, luckily there's the walkthrough pdf to and the skip unseen dialogue option. Unlocked everything again that way already
Edit: HOLY MO... Just run the game again to be sure and it's all locked again!!!
There is, this is what I usually do. I DL the new version, unzip it and paste the old save folder into the new installation game folder (and then if available I place the mods I want, in this game the multi mod). Then I ran the new version without (very important) deleting the old version (or if you just keep the save folder or use the one in the appdata make a back up one because once you run the game persistent file overwrites to the new settings). And I check the preferences menu, if my saves work and if the game have galleries I check if they are like used to be in previous version. If all fine then I delete the old version and/or the backups. This are good preventive measures just in case something goes wrong in the new installation. If happened the issue you got then I would copy the old persistent file again into the new version, maybe something went wrong when I pasted it the first time, if kept the issue well nothing I could do than use the multi mod unlock gallery button or use a universal gallery unlock mod I guess.
Edit : I could also temporarily use URM (universal renpy mod) and check if there is a way on the variables to unlock the gallery, usually done 1 by 1 instance but in some games also work. Once done I delete URM, I don't like using URM in my favorite games because it is very disruptive usually, can be set to be not intrusive but I prefer not to use on a game like Eternum.
Edit2 : Hmm just saw your edited post (sorry just woke up, still sleeping I guess
), dunno what is happening in your game but the persistent file isn't saving your previous settings when you close the game. Your issue seems more troublesome, no idea what can be done to solve it because never faced an issue like that on renpy games. Try deleting the tokens folder in the %appdata%/roaming/Renpy folder like it is suggested in this thread,
Ren'Py - Persistent data not saving upon exiting | F95zone , it may being caused by something you did involuntarily in your windows like it is said on this thread, did any other game happened this same issue? From now on probably we direct message each other for this (conversations forum tool) , moderators may not like we keep being off topic even if this is related to an issue you had in the game Eternum.