score:4
I am a dual citizen, and I regularly check in using the passport other than the one I provided at booking. This has never caused a problem; no check-in agent has ever even mentioned it. So just check in with the passport you plan to use on arrival. It doesn't matter whether you gave that passport information when you booked.
If the airline asks about your other passport, just explain why you changed passports. There is nothing wrong with changing your citizenship.