Your description indicates that you are able to divert the airflow successfully as commanded, to defrost, upper and lower vents, Correct?
Further, it seems that you are able to command temperature changes and all responds as requested, Correct?
Does the noise happen on every selection of airflow every time, or just the first change?
It sounds as if the long HVAC tube connecting the passenger side to center may not be properly secured or fastened, has the heater core been replaced?
It would be helpful to determine what immediately precedes the noise, i.e.
does it happen after you invoke the diversion of air, or as it is changing?
The blend door could bang, but we need to understand is it temperature invoked or outlet invoked?
I am suspecting outlet invoked.
Marty