I got same error too.
I backup using checkpoint then put files in the PC for PKHeX to edit. open up the program, open the "main" file, do a minimal edit for testing (like adding items), Export and replace the Original main. Go back to checkpoint Restore save files, open the game after loading screen with Nintendo's logos get error "The software was closed because an error occurred".
Went back to PC open up the file and get the corrupted error. missing anything? FYI I am using latest version of PkHeX (20200314) and using Pokemon Shield v1.1.1
Update:
downloaded PKHEX (0200214) and went thru the same steps and got the same error. I am beginning to suspect that game version 1.1.1 has something to do with it.
