Hi, I've uploaded a patch that should fix all of the issues which I am able to recreate. I still don't quite know how the prologue party got to be without equipment, and I can't recreate the issue with the saves locking (it works fine for me with no existing save files) but everything else I've addressed.
For the gamepad- if you want to switch back to mouse controls now all you need to do is click the mouse at any point during gameplay (while gamepad controls are still enabled) and it will prompt you to switch back to mouse if you want. The cursor is designed to be hidden for people playing on gamepad platforms (like Steam Deck) so having it visible even with gamepad controls by default can be a bit distracting and problematic. But this workaround should help.