There should be no change to the save files. All of my saves still show up, even from v0.1. You should be able to do like you said with deleting the old one. If you're on windows, your saves should be in %appdata%\RenPy. GnB's saves should be in the folder GlitchesAndBitches-1641348167. If you don't see that folder, your saves might have been deleted.