How to convert Aperture license to app store license?
From an accepted answer by Kyle Cronin from another Ask Different question, with added emphasis:


  From Daring
  Fireball:
  
  
    […] for apps that use the  same bundle ID for the both the Mac  App
    Store and non-App Store versions,  the Mac App Store will not install 
    updates to already-installed non-App  Store versions, but it will
    recognize  them as being already installed. If  you want to get
    updates via the Mac  App Store, you’ll have to re-buy the  app through
    the App Store.