Not sure if this is your problem - but I have come across a similar huge annoyance in that cutting and pasting hyperlinked objects from one document to another - say with a navto:// or an HTMLResource/ reference - maintains a reference to the source file.
A very simple example -
You have a two page folio - it contains an index page and a content page in both horizontal and vertical orientations.
You create an object on the content_v.indd page with a hyperlink back to the index page - navto://index
You then copy and past that object from content_v.indd to content_h.indd
The hyperlink will not work on content_h.indd
If you look closely at the URL of the pasted object in content_h.indd - the URL is - content_vnavto://index
you would expect it to remain - navto://index
but for some reason it prepends the name of the source file to the URL.
There may be a reason for this - but i can't seem to find it - and it creates double the effort - which is a huge deal in creating multi page documents.