Does KLaus know that? No one here knows more than he does - but when you release the D handle and push the top away from the windshield frame, as the hook on the passenger side lets go of the frame, a microswitch in that right hand side opening is relaxed, the switch closes, and grounds a line running to the controller - telling it that the hooks are released.

The pump WILL NOT RUN unless that wire is grounded, for good reason - that is the indicatoin to the controller that it is safe to run the pump, otherwise, the pump could come on while the top is still looked to the frame, which would be bad for the pump and top.

Anyway, as the controller sees that wire go to ground, it sends a message over the CAN but to the BCM to tell it to lower the windows. You just indicated that the windows do not go down, that means the BCM is not getting 'word' that the top is unlocked. If the top controller is not sending that message, then the top controller probably does not KNOW the top is unlatched from the windshield frame - and there is your problem.

Make sure Klaus knows what you told us.