If you could tell us which methods you used I could try to help you to analyze what went wrong.
What I can tell right now: it is absolutely irrelevant which covers are embedded in a file if you want to clear the VLC cache. You can clear that cache any time you want, it is not required to remove embedded pictures first.
In respect to your complaint that you get the covers from the first folder that you selected:
see your other thread for the better way to import covers: Album art