I still don't get
1. how you can expect to cut out bits of a book & still expect internal links to quotes etc to still work. Even if we solved your highlighting issue, that would not work ???
2. why you need to preserve the links anyway - if the link is say to a foot note you just cut out & paste the footnote in-line.
I recall when I was at school how some kids would copy their homework assignments straight out of an encyclopaedia, & not realise that leaving in stuff like ( see also page 69) was a dead giveaway.