They have this set of instructions on their discord server:
**On progress recovery for players on GOG and Epic Games Store**
The patch 1.17 has reworked the save file functionality that will make it appear as if your most recent save file was gone. In reality, your progress is safely stored in a separate account folder. To continue with your progress, you need to do the following:
1. Locate your most recent account folder in AppData/Local/wayofthehunter/Saved that *does not* have the suffix "_GOG" or "_EGS"
2. Copy its contents over to the more recent folder that has the suffix "_GOG" or "_EGS"
3. Launch the game and enjoy!
This worked for me. They’re making all of their announcements etc. on the discord.
Apparently after messing around with it. you need both folders. the one with _GOG and the one without it. If you delete the one without _GOG is deletes and renames everything. I don't know why they decided it was a good idea to automatically delete and rename your save files. It reeks of bad programing. At least it's working again. Let's see if it lasts.