(sorry for the delayed reply!!)
Oh that is really strange??? It sounds like from your description that the "persistent" file is somehow becoming lost? It's this file that keeps track of all the persistent data in the game, such as when you unlock CGs/replays, the title screen update, etc. This is especially weird if all your save files are there and intact, as it means that it's not like the whole game/saves folder is being reset you're just somehow losing only your persistent file???
The persistent file should be in your "saves" folder and look something like this (this is mine from my main game folder):
When it happens that you lose all the data do you see this file somehow disappearing? 🤔 No one has ever reported an issue like this before that I know of so I'm really at a loss as to why this could be happening. If you've played any other games made in Ren'Py have you ever noticed it happening to you before? Also what OS are you using? (unsure if for instance the Mac version of the game might do things differently or something).
(Not sure if it helps, but if you're having the problem where you can't skip because of the persistent file, you can go into the Options menu and choose "Skip Unseen Text" which will allow you to skip things even if the game doesn't think you've seen them yet! This doesn't fix the persistent file issue but it'll at least let you still be able to skip stuff quickly even with it.)