[Frederick NL]

A hanging flap stops the roof from (fully) retracting. Push it up and try if you hear a micro switch click. If so - the travel of the flap needs to be corrrected.

 

[Frederick NL]

Maybe this helps. Switches 126/1 and 127/1 register the status of the flaps. In this document, the section with the photos describes what happens (or not) in the case of failing switches.

 

[Frederick NL]

Flaps not completely opening or closing is a different affair than poor alignment. If you have a broken c pillar cover, it may very well have sagged out of position prior to that happening. The base of the covers must perfectly align with the base of the window. If a misaligned flap causes trouble, simply loosen the screws underneath it and align the flap with the curve in the trunk lid.