So, a weird thing: The changes I made to items stuck, but changes made to Pokemon in boxes didn't. I verified that the time for the main file updated and I restored using checkpoint, but the Pokemon never updated. I then tried reloading from the backup I made and it likewise didn't show any changes.
Do I have to do something more than right-click "set" then File > Export Save ?
EDIT: NVM. I'm not sure why, but when I redid it the same again it saved properly, which I checked by opening a second instance of PKHeX.exe to be sure.