SuranAbus: What do you mean by re-install? Entire game with DLCs or DLC only, because I already tried to reinstall DLC and it didn't work. I have 3 checkpoints: 2 from last story quest and 1 from Kaer Morhen after finishing the game- they are all broken.
I mean a full re-install of everything. It's kind of extreme, but it sounds like you've already done some decent troubleshooting. I don't have a better idea, I'm afraid, than starting from a fresh game install.
Interesting that you have broken saves from before the DLC should take effect. That sounds like the sort of problem that comes from badly coded mods. Were you using any game mods, by chance? If not, then...then I have no idea at all. Sorry.