Sadly, I've found that it's more efficient to keep a few lesser developed OMEGA residences that only require 1-3 OMEGA items to develop so I can refresh the building plans on these lower buildings to consume the few OMEGA items that I don't "need". Once these residences start requiring more complex combinations of OMEGA items, I then bulldoze those buildings and replant them to start the process all over again.
It's a less than optimal technique for using up OMEGA items, but it gets the job done. It allows me to be able to use up specific OMEGA items while retaining the items that I need for upgrading OMEGA Storage and NeoBank.