Aperture 3.5.1 on OS X 10.9.2 hangs when trying to update the backup

Aperture 3.5.1 on OS X 10.9.2 hangs when trying to update the backup. I get the rotating beach ball cursor for hours but not get the confirmation dialog known from 3.4.2 aksing whether I really want to back up.
On old Mac Mini with OS X 10.6.8 and Aperture 3.4.2 there was no such issue.

Creating a new vault and populating it always works but then turning around and updating that vault hangs? The drive is formatted OS X Extended, correct?
That is strange. Before abandoning vaults, they should and do work in 3.5.1, I'd try this
Run a library repair on the library. I always do this now as it seems to cut down and hangs when updating a vault.
Before starting the vault update open the Aperture activity window Aperture->Window->Show Activity.
Now do the update.  I can't give you anything specific to look for, just try to get an idea of where the hang is happening (if it happens after the repair).
As for rsync, it should work OK but keep in mind as a lot of the data now in 3.5 is in database files any change to Aperture will result in reync seeing a lot of files has having been changed so I'm not sure now much of a savings that will be over just copying the library. To be honest I've never tried rsync on an Aperture library so this may not be an issue but something to keep in mind. BTW do you have much rsync experience? It can be a bit of a bear to setup if you're not familiar with it.
Another option is to look at one of the cloning programs Carbon Copy Cloner or SuperDuper. They have the ability to make clones and then update only the changes since the last clone operation. In reality, I believe one or both actually use rsyn as the backend but give you a much nicer way to set it up and schedule it.

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