Did you accidentaly press import from rebirth and lost your afterbirth file? If yes, I got a noob solution that worked for me.
Recovering Your Save
First, turn down Steam Cloud save.
Then go to the remote folder which should be under Steam-->Userdata
Make a back-up of the folder in case anything goes wrong and then proceed to erase it all except:
- since these are your Afterbirth+ savefiles.
Launch the game and you should see the file you deleted, if so, proceed. After that, start a run and keep the game open for a while. Then close it.
Turn on cloud save and launch the game, you should see a message saying that there are older files in the cloud than in your pc so you got to choose either uploading the new files or downloading the old ones.
Choose upload newer. Problem should be fixed.