My air cycle and control system will not cycle out of the window defrost mode to vents or foot vents. It does cycle through hot and cool and inside air and outside air. This vehicle has the nav system and the cycle controls are on the nav screen?

Sounds like a vacuum problem! I would have a Tech go over all related items near the trans repair.

Hello, first, I don't see any correlation of the transmission replacement to the concern you are currently having. Of course, it is difficult to say and all installation work done should be inspected to ensure no wiring / vacuum lines were left loose or something like that. Testing of the climate control system will be needed to find out if there is a problem with the mechanism that controls the movement of the mode door, which directs air flow to the desired location. Sounds like the temperature blend function is working as it should be.