MOSTAPPS SHADOWED AFTER BIG SURE UPDATE

Safe Boot, (holding Shift key down at startup), does the problem occur in Safe Mode? Could take 10 minutes.

Safe mode attempts to repair Disks & clears lots of caches & loads safe Drivers, & prevents loading of 3rd party extensions, so if Safe Mode works try again in regular boot.

To find out if it's system wide or user specific, try this...

Open System Preferences>Users & Groups, unlock the lock, click on the little plus icon, make a new admin account, log out & into the new account.

Does it work in the new account?

Are the installed Applications / Extensions compatible with Big Sur. Check with the Developer for compatible Apps / Extension or do they offer updates. Same goes for Third Party Drivers for Printer, Scanners etc.

If upgrading from Mojave and earlier versions of macOS - Remember that Big Sur does not support anything 32 bit. These include Applications, Extensions and Drivers for any devices. There is no workaround.

Hmmm, I wonder how they got deleted?

Have you re-added some Apps & they work now?

Start with this...

Safe Boot, (holding Shift key down at startup), does the problem occur in Safe Mode? Could take 10 minutes.

Safe mode attempts to repair Disks & clears lots of caches & loads safe Drivers, & prevents loading of 3rd party extensions, so if Safe Mode works try again in regular boot.