When the car has warmed up and I'm driving about 40 to 50mph I start hearing a flapping sound. It sounds like a flat tire noise...I can't tell if it's coming from front or back but it's loud like riding on a flat tire.

That's going to be difficult to find! .. There's something that IS actually flapping from the 40 + mph wind traveling around the vehicle.. Look all around for ANYTHING that may be loose and causing the noise.. Been there done that.. Be supprised at some of the things I've found over the years!