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I saw this update but it doesn't mention this problem specifically, and the Apple support page reporting the issue has not been changed.
 
Apple have updated their advice to state that you should exclude your Aperture library from Time Machine, it should then be ok to use Aperture with Time Machine on auto.
 
I've excluded my Aperture Library - but what about vaults? I have a vault, and would like time machine to at least back that up.

It's absurd that nobody at apple figured out that Time Machine wouldn't work with Aperture. My photos are probably my most valuable data on the machine!!
 
Sucks that the new Aperture doesn't support Time Machine like iPhoto does, I was hoping to zoom around my deleted Aperture library.
 
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