I tested this with b2gpopulate. The test case isn't exactly was you described so I created it by renaming some music files to 3gp and then removing the video files caused the audio files to be removed too. but b2gpopulate won't be affected because the file types are isolated by filename rather than just interpreted type.
(I did note that b2gpopulate probably won't work against a flame due to hard-coded paths and this pull request will help that).