Stawe: After several days without problems, Risen just didn't want to start today. Tried "Repairing" it, didn't work so I figured I just reinstall it. I double checked to not click the "Delete all my saves aswell" option since I wanted to keep playing afterwards.
Problem now is that my Saves are indeed gone and there aren't any Cloud-Saves. I tried downloading them through the "Extras" Tab but its just an empty folder even tho I had Cloud-Sync enabled and had no problems with it until now.

Is there a way to restore older Cloud-Saves or any Cloud-Saves at all? I doubt there is a way to restore my local saves since GoG just decided to delete them so Cloud seems like my only option here.

SCPM: Before the latest game update Risen saved files to 'C:\Users\%USERNAME%\Saved Games\Risen', check that folder to see if you still have any save files located there. After the update, the files I believe are now located in 'C:\Users\%USERNAME%\AppData', there should be a Risen sub-folder in either \Local or \LocalLow or \Roaming, I don't remember which.

Stawe: Found the save folder in Local and sadly its empty. So seems like GoG just deleted them together with the game.
Tho whats strange is that I still have all my ingame Achievements when I check them in the main menu.

Kinda sad, really enjoyed the game and was 20 hours in. Maybe at some point I'll start a new run.
But thanks for the help