I don't know a way to fix this without redoing something. How many not-reconnected Images are there? You can try this:
- copy the not-reconnected Masters
- change the not-reconnected Masters to the _exact_ file name that each Image reports as it's Master
- try to reconnect to the newly renamed Masters
You can also re-import the Masters no longer associated with the Images-missing-Masters, and then Lift & Stamp the adjustements and metadata from the Images-missing-Masters onto the newly created Images (and then delete the old orphaned Images).
Weirdly, Aperture has gone on and dis-associated the Master-Version pair for some of the one I have done this to.
You should, of course, move Masters _only_ from within Aperture (but the problem can occur even when you do).
I've seen problem with less than a dozen Images out of several hundred thousand spread across a few Libraries (i.e: something like 1/400 of 1%). I haven't carried my trouble-shooting any further.