Hey, I've just found another issue:
After meeting the quiz wizard (which was after the cutscene of the meeting with Elene) I noticed when returning to the inn that the yellow arrow that pointed to the Elene meeting area was still present, so I went there and then something funny happened: it all looked like the begining of the Elene meeting cutscene (Elene was there looking towards the water and Leonardo wasn't in the scene yet) but it didn't advance at all. I thought that the game was frozen, but after seeing that I could enter the menu and seemingly move the "camera", I soon understood that what happened is that Leonardo's sprite had disappeared; I was just controlling a "disembodied" Leonardo.
I also tested playing like this: you can't interact with "frozen" Elene, but you can talk to the innkeeper and go to bed as usual to progress the story (as long as you manage to navigate through scenery obstacles while invisible), and only after the Luna cutscene and battle Leonardo becomes visible again. I also found out that if you enter the Tournament Area just before the Luna cutscene you can't return to the main map at all, but I don't really know if that's related to Leonardo being invisible or if it's a bug on its own.