I have the same problem! I just downloaded the new fix, installed it and the progession of Hoan, Suplex and Punt disappeared. I haven't finished them all yet but now they are fully hidden again.
Edit: I noticed that the heart I got for finishing Hoan's story was still there eventhough I couldn't open it because the face was blank. I used the gacha button a couple of times to gain back at least one of the original residants and I got Hoan. All story progression was lost BUT I still could play the FINAL.