Saves and Moving to a New Version of the Game
First I want to say that game saves will inevitably break. It's the combination of both how Renpy works and how I set up the quests as well. If you save in the middle of a quest and that quest changes between version there is a high likelihood that something will break when you try to finish that quest on a new version. I try as much not to change previous quests but some things need to be fixed and I would rather rip the band-aid early and fix those bugs/issues rather than leaving them in the game for prolonged periods of time.
Safe Way to Update to a Newer Version.
For you to have as smooth transition to a new version as possible, I would advise you to do the following: Complete all of the content in the old version and when every single quests says: "THE QUEST ENDS HERE FOR NOW" than you know you have reached the end of that version and it is safe to switch to a newer version. Otherwise the game might break and stop functioning properly.
Chapter Feature and Cheats
Also I want to remind you that there's a chapter feature that allows you to skip parts of the game you have already finished. This pairs up nicely with the previous approach where you finish all the content in a previous version first. The chapters start at the exact end of the previous version allowing you to basically think of the chapters as a clean save at the end of the previous version. This gives you the ability to start where you left off, without the risk of encountering these save breaking issues.
Also there are cheats to let you tailor the game experience however you want. However, I want to stress that the game is balanced and intended to be played without the cheats. The cheats are there for whoever wants to use them, for whatever reason.
And one last thing. Please report any bugs and issues and I will try to fix them as soon as possible. But also please take note that saves will break and that's something I won't be able to fix retroactively.