This is a dramatic step, but I’ve found that it works in situations where nothing else will. This should only be done after a full repair and rebuild of the Aperture database have proven unsuccessful.

If you import your entire Aperture library into a new, empty library, it appears to basically rewrite the entire database in a way that is superior even to the rebuild command. You’ll probably need about double the size of your existing library as free space to do this (meaning if your Library is 250GB, you’ll likely need another 500GB free space for this). You may want to do this to an external drive.

Simply create a new Library in Aperture by going to menu File > Switch to Library > Other/New… and creating a new one from there. Then, go to File > Import > Library/Project… and select your old Library.

This could take a very long time. As in, overnight.