If like a lot of players (including yours truly), you weren't sure when you launched Repentance that your Afterbirth+ save had been correctly imported or if you had the misfortune of clicking "Import save from Rebirth", follow this guide to make sure you'll be playing Repentance from the point you left Afterbirth+.
Step 0: You may launch Afterbirth+ (deactivating Repentance in the DLC tab of the game's properties) and check/take a screen shot of the stats data screen.
Step 1: Shut Steam down to prevent any cloud synchronization during the process.
Step 2: Go to the folder of the remote saves of Rebirth (Steam install folder).
Remote Save folder in Windows 10.
Step 3: Better make a save of your current files, use your preferred method (copy elsewhere, zip the files, etc).
Step 4: Note that the save have either a prefix (ab_ for Afterbirth, abp_ for Afterbirth+, rep_ for Repentance) or none (for Rebirth) and represent the save slots in the game for each version.
Step 5: Delete the saves from Repentance (starting with rep_), if any.
Step 6: Copy the files from Afterbirth+ (starting with abp_), and rename them as they were (removing "copy of") but replacing the prefix "abp_" with "rep_" to make them the save files that Repentance will use.
Step 7: You may launch Steam then Repentance.
Step 8: Go to the Stats screen and check them to see if they are the same than in Afterbirth+. You may do this now by following Step 0 (no savefiles will be deleted).
First two saves are "imports" from Afterbirth+, last one is empty save (0%).
You should now be good to go!