I could be wrong but I think as long as you don't claim the box (taking the exp, dust, 3rd item) you'll be fine. If I'm wrong someone please tell me.
Aerodactyl was a specific quest for Let's Go so I wouldn't think it would change. If you wanted to be safe you could just stack it by claiming the research now then fleeing from the encounter. It will remain available to encounter again whenever you want to and won't change based upon research changes.