See bug #695747 if we have an input PDF file with Named destinations (stored in a Names tree) we don't attempt to preserve the Named destinations. Instead we dereference any annotations which use the Named destinations and embed specific Dests.
This is fine for a stand-alone PDF file, but if any external file references the produced file via a GoToR (Go To Remote) link, then that will fail with the new file, as we didn't preserve the named destination.
Instead we should preserve (or rather rebuild) the Names tree, and as an enhancement preserve the names in any links which originally used them.
*** Bug 696943 has been marked as a duplicate of this bug. ***