The Remove Annotations feature is a good enough response to the feature request made here in UserVoice:
http://logos.uservoice.com/forums/42823-logos-bible-software-4/suggestions/1124125-selective-erase-for-highlight#comments
The only big gap is that I'd wanted a way to toggle a specific highlighting style on/off [like removing a layer in autocad). However, doing this manually is no longer as terrible as it was before the Remove Highlighting [Annotations] feature was added some time ago.
I suggest Logos mark this one as "Complete" in UserVoice