I've never heard of scenes disappearing from the gallery before. They're saved with each save file, so even if you create a new save, the unlocked scenes should still be there.
The system just checks if a scene has been viewed and then adds it to the gallery—it's a pretty straightforward process, so not much can really go wrong.
Did you happen to delete your persistent files or anything like that?
Viewing post in Lewd Lore: Isekai Fantasy comments
Yes, it seemed strange to me too, but even scripted scenes like the first one with Aveline were deleted. Well, I reloaded a save and with Aveline it's fine, but for Isabella, still the same problem. Afterwards, it's possible that it's a problem that's just specific to me. In any case, very good game, courage for the future! ;D