normally this problem is because of corrupted save files not containing what key those assignments bind to
try and see if there are any files called save in this directory:
"AppData\Roaming\Godot\app_userdata\Empty Shift\saves"
if there is, delete it and open the game again
another solution could be you yourself going in options in the main menu and setting the keys up again which might work
let me know of what happens, i have to fix it if its an issue from the game!