I use the following technique:
- Select all (CTRL-A)
- Use Edit Meta
- Click on the button against Add Tags to bring up the Tag Editor. This shows all tags and I can select those I want removed.
- On exiting the Tag Editor cut the string that is now in Add tags across to the Remove tags input box
- Press OK to remove the selected tags from any book that might have them.
I am not sure why the Remove tags input box does not make the Tag Editor available as it would be convenient.
You can later do fine tuning by typing in tag:tagvalue into the search box to see what books have a particular tag (when you do not want it deleted from all books) and select just those required. You can then bring up the Edit Metadata dialog and proceed as described above