How to ignore second hard drive
I have a similar configuration. Two physical drives: one Mavericks, the other Mountain Lion as failsafe. When Yosemite comes out, I can leap Mountain Lion ahead.

In your primary OSX, exclude the /oldpartitionname/ (or, /oldpartitionname/Applications) from Spotlight.

Then reset "Open With" menu with Terminal:

/System/Library/Frameworks/CoreServices.framework/Frameworks/LaunchServices.framework/Support/lsregister -kill -r -domain local -domain system -domain user


Your OSX will rebuild a new list of apps, within the newly defined scope.