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My understanding is that once a savefile becomes corrupted and the game tries to load it, it's effectively gone as the game will soon save the fresh level 1 savefile data on top of it.
This is why I made the backups addon .dll you can find in the mod description tab - once installed, it creates backups for you when starting a run, and once data loss is detected (checks that you're back to global lvl 1), a prompt shows up when opening the tree that lets you try to load an existing backup.
Mod data savefiles themselves are found in the Isaac installation directory, under "data/passive skill trees/".
https://steamcommunity.com/sharedfiles/filedetails/?id=3354574692
and while I'm run, I get this error every frame:
https://steamcommunity.com/sharedfiles/filedetails/?id=3354577914
Unfortunately if the addon was installed after the data loss then the data is very likely irreversibly gone at this point, but this error chain could use fixing.
As a temporary measure, you can try moving your "save1.dat" file away from the saved mod data folder (Isaac dir -> "data/passive skill tree/"), so the game can gracefully regenerate one.
it is shown in these screenshots:
https://steamcommunity.com/sharedfiles/filedetails/?id=3354655844
https://steamcommunity.com/sharedfiles/filedetails/?id=3354656593
https://steamcommunity.com/sharedfiles/filedetails/?id=3354656947