Yeah the remove option of Mp3tag seems not really designed for FLAC files... So I googled and came up with an application called Tag. You can find it at http://www.synthetic-soul.co.uk/tag/ The discussion about removing ID3 from FLAC files is at this link on hydrogenaudio forums. Most important is the switch --removeid3v2. Works fine (it's actually a very simple file operation). See the thread for more usages like handling all files recursive and so on.
Can you do multiple files in one pass with the switch? What do I put in <files>?
OK. I found a method to remove ID3 tags that are with FLAC files.
When use Mp3tag to remove ID3 tags, it removes all tags including the FLAC tag. But if you choose Undo, it restores FLAC tags only. The only thing that I have noticed that isn't restored is the cover art. So you will need to restore that manually.
If anyone knows a better way, I would be interested.