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The best you can do is sync the game data with your steam achievements by going into Stats and pressing Alt and F2 at the same time. It doesn't restore completion marks, though.
https://github.com/jamesthejellyfish/isaac-save-edit-script
If you're uncomfortable with Python just download the executable version in the 'Running' section. Once you have it you should open two seperate instances of it. Your save files will be located in Steam\userdata\[yoursteamID]\250900\remote and you'll see 'rep+persistentgamedata1.dat' and if you started repentance you'll find 'rep_persistentgamedata1.dat', if you don't have one then just start a quick save file on repentance. Open each of them on different instances of the save editor and just use the repentance+ file as a reference for what needs to be checked on the repentance file. It will take a while going through all the secrets and item collections but it will copy across all of your progress. The only problem is that any completion marks you turn on will be considered hard mode/greedier checkmarks.