I had this happen to myself around the the time repentance released. I played around with the save files and then found the fix that way.

If you want to read trough my original post then here is the link

https://steamproxy.com/app/250900/discussions/0/3068614788766361287/#c3068614788776759141

You can find what I said further down in the responses.

First things first, you go to your c://documents folder and search for the "my games" folder (don't know if everyone has that folder named that way).








If you did it right it should look like the picture above.

Step 2
Go into the "Binding of Isaac Repentance" folder. It should look like this.




Do a backup of this file, as this will be your last chance to recover your save file







Looking at the files you should notice something.














The 3 files at the bottom, persistentgamedata1.dat , persistentgamedata2.dat and persistentgamedata3.dat are your current save files in the game.

The ones that have numbers infront of them are old save files.
If you look at the numbers of the old files it tells you a date on which this "backup" was created.

The first thing you have to do is to delete the current save files




We do this because these are blank/the wrong save files.

Then we search for the files when they last worked correctly.


Lets say in my case those where those from the 8.04.2021






What we do now is to rename those 3 files. We just cut off the date at the beginning.









As an extra step you can delete everything in the folder, besides your new "persistentgamedata1/2/3.dat files.

Now load up the game and you should have your save files back!

If you messed up then just copy and paste the files over from the backup you made and try it with an older "persitentgamedata.dat" backup.

Give this guide a thumbs up if it helped you!
It gains visibility that way and others with lost save files will find this guide more easily.