Besides this question I’ve also read your other topic where you bring it up.
Considering the damaged .mlt file, I wonder if the source files location are somehow bad? However, Shotcut would then ask for the location…
Or one particular property of the source files is maybe bad?
You can open the .mlt files in notepad or similar. What if you make a new bogus project with the originating file, just do one cut for the record, save it, and compare the .mlt file with the bad .mlt file.
I don’t know if it brings you something but it is something you could try.
Another thing you should do is clear the Windows temp folder just to make sure no remaining Shotcut files get in the way.
Just enter %temp% in the address bar of the Windows file explorer, then select all and delete it by pressing shift+del. Note this is irreversible but emptying the temp is no problem.
There may be some files in there used by the system but the system then will prompt you and all you have to do is skip.