When you run Itch version 39, what number is in the bottom-right of the Title screen? (Itch has it's own version numbering, so I'd like to see what version does work for you)
At some point we did change the way our save files worked, which may be why you have 2 folders. If you rename those folders and try the new version, does it still crash? If so, there might be something wrong with the old save data that is not loading properly... we tried to make sure that every version was compatible with the one before it, but if you hadn't played in a while, there might have been something in a build you skipped that was changed? Not sure...
IF the new update does launch with the renamed save folders, then we have 2 options:
1: If you don't care that much about progression, and don't mind starting your save file over, we don't have to do anything, you can delete the old save files.
2: If you want to see if we can save your old data, then let me know which folder was re-created by the working version, and then email the old version of those files to me so I can pick them apart. This might take some time to figure out where the problem is, but you should be able to recover you saved data once we figure out what went wrong - and it may help someone else in the future.
Totally up to you!
If the save files DON'T fix the issue then I am really stumped...