“Will save files from Afterbirth+ be compatible? I know some other games, such as Shantae 1/2 Genie Hero, have had compatibility issues due to to including the DLC on the cartridge.”
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If you have previously purchased Afterbirth+ on the switch's online shop, then there is a possibility of the save files merging. Despite this, with the cartridge form of the game, I do not believe that save files would be able to transfer between games. I believe the best option is to wait until the DLC releases on the Nintendo online shop to avoid possible save file errors. Side Note; I feel obligated to encourage the support of playing the new DLC in a new save file. The creator of Binding of Isaac, Edmund McMillen, vouched for the idea of playing Repentance in a new save file.
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