I didn’t say that avast doesn’t support ME, ME doesn’t support boot scan, a limitation of ME not avast.

You haven’t said why they were not scanned? Give an example of a few (not all 2000), they are more likely to be in groups of the same reason, etc.

There could be many reasons, password protected, in which case avast doesn’t know the password so can’t check them. Some programs encrypt or otherwise protect their programs/files.