You are not alone in this bug. This bug has been the bane of my existence. It is only triggering in some routes but not all the others and I'm trying to go back through the coding and find the specific area where a previous code did not trigger for this scene. I think I may have found it so it should be fixed in the next week, but it has been a painstaking process to find. LOL! I'll post a big patch update when I finally get it to work.
As for the saves, I'm not sure what happened. Nothing in the recent update should have deleted anything prior. The only time I know that happens is if browsing history or cache is cleared. But if you didn't do that, I don't know if it was a glitch or a weird fluke on itch.io. If it happens again for some reason, please let me know. But none of my coding should have broken a game so far. I'll ask around and see if it has happened to anyone else too. Maybe there is something I'm missing.