Learn to use this feature:
View attachment 2657684
In the options. Works for nearly 90%+ of the games on this site.
It allows you to skip text the game doesn't think you have seen even if you did and just turn it off when you get to the new update part.
As for Appdata should not be touched when you update the game even if you completely download the whole game again for each update so your saves should be usable still unless the dev changes something major.
As for when you copy saves there should always be 2 files you copy. Never 1.
If you are overwriting or using an old save make sure you have it saved with the right name i.e 1.1 or 1.2 for save slot 1 or 2 etc.