Regarding the stats, that sounds like it's just the most recent update. Enemies now gain free points of Attack every stage and their attacks have higher power weights. (If they almost defeated you but you were still able to win, then it's working exactly as intended! You're fully restored after every battle, so I wanted individual battles to be more difficult.)
This is not the first time I've reloaded/loaded a save, but probably the first time where I had after manually putting stones in the door slots and having left them there.
Then that must not be it; even if there was some weirdness with your save not getting initialized correctly the first time, it should have updated to the current version on your first load.
I'm sorry, but I really have no idea what could have done this. The only other code that interacts with the door slots are the options to add and remove keystones; there should not be anything that affects them remotely. When I reload my own pre-Amethyst save, the keystones are still there, so I can't replicate this.
I've added a save update that should replace the keystones in your inventory. It'll be included in the next update, which will go live this afternoon.