A theory. I think this may be inevitable if you merge the SAME file.
Realise that bookmarks don't have a page range; they have actions - usually go to actions with a destination. When they have a destination, the page containing the destination is thought of as the target.
Most bookmarks in common use have specific pages as targets. These can be managed in merging.
However, FrameMaker is smart. It uses named destinations for links and (I suspect) bookmarks. These use randomly assigned names. This specifically allows books to be assembled in PDF in a very flexible way, because the destinations do not change as more is added.
But you may have found a particular weakness. If you merge files with the same named destinations, only one can be left, and it may be random which one.
You haven't just broken the bookmarks, I suspect. Check the links too.