Thanks very much for that post Mapline. I haave not been able to use SQSpyLite to have my cover back however. So I was wondering if you could explain what you mean by:

"I don't actually use this as it requires you to unpack the book, repack and so on and that's to much work for me so I just modified kiwidude's Modify Epub plugin for calibre to do this for me."

Is that version of Modify ePub available somewhere? or is it just specific settings? Also, would that fix the problem with annotations?

Many thanks