Thanks for the original posting ddiemont and for the last two posts from imartin42 and mikejackson16. I had the exact same scenario with purchase of Aperture CD version from Apple store back before app store and no record in app store and update not being allowed after Yosemite install.
It took two calls to Apple Support to finally make it happen. The first ended with there was nothing that the App store could do because I bought it from the Apple store and the Apple store saying the App store can now only issue Aperture. After finding the last two posts in this thread I called back and refereneced them and some action started to happen. It took a good while getting info and checks on Apples end, but my phone rep, Timika, working with the App store made it happen. Phew and yahoo! Download went through with redemption code and Apeture now appears under purchases for easy future updates.