Hi,
That does sound like something that would solve it. I will check if I remembered to take a backup before I updated the file_stage fields. If not, I will do another test upgrade on Friday anyway.
I still have to solve this as well in the next upgrade test: OJS 3.0 upgrade fails to move/rename some supplementary files
I will probably look for a script that will change the extensions to small case and run that before the update, but I think that the issue mentioned there is something that should be taken into consideration also in the upgrade script.