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Mantano does what you want. When it says "importing" its not actually making a 2nd epub copy, just making database records for highlights etc. as for its expensive "cloud" service, just don't buy it - it's an optional monthly fee extra anyway.
if you delete a book via CC though, mantano bookshelf will still list it, greyed out i.e. it will know it has gone but will not delete any associated notes, highlights etc unless told to. that's probably a good feature ?
of all those ones I tried, Mantano was most respectful of book CSS,; Moon + makes far too many arbitrary changes for me.
the Kindle fire native app would be ok if I could configure screen tap zones, for left handed use, but that's not allowed. ditto for Kobo android app.. so I have done my best to mimic the Kindle app line spacing and background colour themes in mantano
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