VanishedOne: I seem to have a copy of the save directory under C:\Users\[MY ACCOUNT NAME]\AppData\Roaming\FALCOM\ED6 I'm unsure whether it's a distinct copy or just an alternative file system path, but you could have a look there.

nightdrgn: For anyone arriving here trying to play the game.

If you have BOTH steam and gog version you might see the gog version get completely confused on which version it is. I don't know what causes this but you'll see things like the title of the program show as (GOG) (Steam) at same time.

First, lets get your saves back. If you dont find them in your gog save dir they're likely in your steam save dir.

GOG saves them in %appdata%/Saved Games/FALCOM/ED_SORA3

Steam saves them in <Steam Dir>/userdata/<your-user-id>/251150/remote/TC

On linux you may need to go to <Steam Dir>/steamapps/compatdata/436670/pfx/

Your save files will be in one of these locations. Just grab them before things get even more broken.

After you do remove both locations so that the game doesn't have a chance to get confused.

Go to your GoG Config3_DX9.exe, open what it says is the save folder and then paste your backups there. If you previously had saves on gog some will work on steam some will completely crash on steam. So its safer to not mess with it. Incidentally the steam version will have similar issues.

Now when you start the game make sure you ONLY see (GOG) in the title. If you see nonsense like (Steam) as well or both then close and start it back.

If you still have troubles getting it to work properly one sure fire way is to close both steam and gog galaxy and then run the game, that usually prevents it from going crazy.

Hope this helps someone.