Is it possible to quickly clear flags in Apple Mail 6 ( probably with AppleScript)?
According to this thread, copy below script into Apple Script Editor and then run

tell application "Mail"
set selectedMessages to (selected messages of front message viewer)
if (count of selectedMessages) is greater than 0 then
    repeat with theMessage in selectedMessages
        set flag index of theMessage to 1
    end repeat
end if
end tell


Your selected message will flag with Orange. You can flag message with other color by replacing 1 in the script