delete all 4 files in the picture from config.json to titles.sha. let checkpoint reload everything properly. if you can backup correctly again, repeat what you said. copy and overwrite a restored save into the ssb folder, you might also open ssb before using checkpoint to see if it says something like in my case "unable to use the save". otherwise you should backup the save with checkpoint, restore it immediately after and test the game. if checkpoint wont work correctly again, delete those 4 files again.