I found myself in a situation where I had to rename the anchors in a document (I'm using cross-references to paragraph destinations pretty much exclusively). I had to merge some documents that had all been cross-referenced, and (somewhat surprisingly) ID didn't know how to handle that and so my cross-refs ended up pointing to the wrong things. I successfully renamed the paragraph destination anchors and the destination names of the cross-refs themselves (I did this through scripting, but I don't think this is a scripting issue).
The problem comes when I export to PDF, either as print or interactive. Most of my cross-reference links don't work, because they are still pointing to the old anchor names. So, for instance, I have a cross-reference that, in ID, is pointing to Anchor 27, and Anchor 27 exists and is the correct destination. But in my PDF, the cross-reference is pointing to Anchor 14 (presumably its original destination). And it doesn't even go to the wrong place, because it still has the old sequential reference as part of the anchor name (so the full anchor name is something like "test.indd: Anchor 14:14", whereas the actual Anchor 14 is named something like "test.indd: Anchor 14:10").
I've tried restarting InDesign and even bringing the file onto other computers and I still get the same, very wrong, result. This must be a bug of some kind, but I have a deadline, so I'm hoping someone has encountered this and might have a solution. I'm a little bit in shock that such a huge bug could exist, so with any luck at all I'm just missing something here.