Beware: if you run Lion on a separate drive, don't update aperture

I'm not sure how MacOSX managed it, but I ran Aperture tonight (on SnowLeopard) and it tells me that I can't run this version of Aperture on my operating system!
The problem is, I never updated to the version it was claiming. The AppStore prevented me from updating to the "Lion Only" version. So what happened?
I have Lion installed on another drive. It has nothing to do with my Snow Leopard drive, there's no connections to it. But after I updated Aperture on that drive, on Lion, it must have decided to update my Snow Leopard partition as well - and bypassed all the obvious problems with that.
TimeMachine came to the rescue, but still. I'm surprised Apple could find a way to corrupt my installation this way.
AppStore runs around all drives looking for Application folders to update, regardless of OS?

Sounds to me like the launch services didn't use the version of Aperture in /Applications on SL but launch the one on the ML drive instead.
TimeMachine reverted the library back to how it was previously, so that rules out "having been opened by 3.3"
One way to test: pull the other drives other than the one with the OS you want to use or test with.
Pull the drives and leave only one. I assume you would also clone your systems for backup so you have working untouched off line copies of each using Carbon Copy Cloner or another.
Merging libraries iPhoto libraries in Aperture
Note: Before you start, you must have opened each iPhoto library you intend to merge at east once in iPhoto 9.3 or later.
To merge the libraries:
Open Aperture 3.3 or later.
Click the File menu and choose Switch to Library > Other/New. Use the library selector to choose one of the iPhoto libraries you'd like to merge.
Choose File > Import > Library
Select one of the remaining iPhoto libraries you wish to merge.
Repeat steps 3-4 for each additional iPhoto library you wish to merge.
The library you started with in step 2 above includes content from all the merged libraries. The other libraries are still present (and useable) on your computer. Once you have confirmed that the unified library is working correctly, you may wish to remove the other libraries from your hard drive. It is a good idea to back up all your libraries before doing so.
https://support.apple.com/kb/HT5296

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Beware: if you run Lion on a separate drive, don't update aperture

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