How do I stop my Mac seeing/loading apps on my cloned backup HD?

I have a spare hard drive which has a backup of my Lion installation from before I upgraded to Mountain Lion. I created it with Carbon Copy Cloner. How do I stop my Mountain Lion from seeing the apps on that hard drive?

App Store is seeing those apps and thinks I have stuff installed. I don't want those apps to ever be used or seen.

Clone over it with ML.

I was going to do that but i was hoping to wait a while to make sure I am cool with everything in ML.. I didn't want to have to disconnect it

I'm not sure that's what the app store is seeing. Only way to know for sure is disconnect the external drive and then visit the app store to see if they disappear from the options.