I've also discovered this problem, but unfortunately don't have an up-to-date, pre-update vault from which to restore from.
I have a 15G iPhoto library that I am trying to merge with a 49G Aperture library (granted, most photos are duplicates, but until now, that's been my only easy option) and when I try to merge as per the instructions, I'm informed that I need 4 Terabytes of disk space to do so. Which is, well a little excessive I would have thought.
I have deleted all iPhone movie files, emptied both trash folders, rebuilt both databases and I'm still finding the same issue.
If the above is anything to go by, am I best to create a new vault now and restore from that, or go back with Time Machine to before I upgraded the Aperture library, restore the old Aperture library, create a new vault, then restore today's Library from that new (old) vault and manally re-add the photos added in the meantime?
Sounds like a bit of a silly way to do things.
I'm guessing it would be easier to try and identify which photos are in iPhoto that aren't in Aperture, import those by themselves, and use the Aperture library in iPhoto from here on?
Anyone else remember the good old days when Macs 'just worked'?