Can I update an Mac App purchased by a different Apple ID?
I recently ran into this issue in a different context.  I changed my developer appleID and had xCode registered under the defunct one.  When I upgraded to Mavericks, Xcode wouldn't update, since I'd downloaded it from the Apple store under defunct AppleID.  

I removed the association with the defunct appleID by removing the receipt from Xcode:


Control-click Xcode app and "show package contents".
Move the _MASReceipt directory to the trash in order to dis-associate Xcode with the old AppleID (you'll need your Mac's admin password).
Restart Apple store and "install" (rather than upgrade).


The net effect:  Xcode will "install" (upgrade) but under your preferred AppleID.  

You do NOT need your ex-employee's personal AppleID account for this, but you do need admin rights on the machine.