Is “Delete Duplicate” offered by iTunes Match different from simple deletion

It's been confirmed elsewhere that metadata alone will not give success in matching (if it were, someone would quickly find a way to just create thousands of dummy files with the right metadata). Some audio fingerprinting is going on, and you can test it by changing the metadata of one track to that of another one, and see if if matches the audio or the metadata. Still, metadata plays a role as well.

MacWorld have a note on the problem of one or a few songs not matching from an album: Basically, it seem to affect specific songs (rather than just randomly failing every n:th song). Two possible reasons for this:

1. The audio or metadata specific to that track confuses the matching algorithm (as we know, audio fingerprinting is not an exact science)
2. There is a rights issue with particular tracks that Apple haven't been able to find agreement for.

I might suggest a really wild -- possibly dangerous -- approach. If you have a good backup, it is less dangerous, but until you have restored from that backup there still can be snags and problems in a restore that you want find until that point. The good news is you don't need the backup, it's just there I case a crash happens in the middle of this process.

• First make sure you've got a good backup of your iTunes library.
• Then delete all your apps from iTunes.
• Finally, sync each of your iDevices and when it tells you it found apps on the iDevice(s) that were not in the library, make sure you tell it to restore them back to the library.

You should end up with only those apps that are installed on at least one iDevice! (In theory, at least.) And if anything fails, restore the library from its backup.