As of the most recent update, the app keeps track of which games pokemon deposited are from via a separate pokedex, and even offers a reward for completing some.

Either adding a completely new segment below the Shiny Alt Forms to include all the pokedexes (since they don’t need to be shiny). Or possibly similar to the current markings you can give the pokemon like “trading for,” can receive an overhaul and allow markings to be put below pokemon to “check off” which games they can be found in.