I was very tempted to just push this live already but given my recent track record with it some additional testers welcomed...
Changes for this beta version:
- When choosing Remove existing cover, ensure any NCX and internal TOC links are removed.
- If a user chooses one of the redundant options, don't run it.
I've chosen option (3) of those I presented in the posts above. It doesn't preclude me from also implementing option (1) of the checkboxes unticking themselves at a later date if people say they want it, but right now it stops the plugin from doing extra work or having unfortunate side-effects.