When I run a full scan, tons of files are noted “can not be scanned because file is password protected”; I can’t tell how many files ARE scanned. What does the message mean? Are the unscanned files vulnerable?
They are files that are password protected, such as items related to known, safe programs. The files can not be scanned unless the password is supplied.
Once the password is supplied by what ever program is using these files, avast! will check the files when they are actually run.
While they are in their password protected state, they pose no threat to you or your system.