The tops have a number of position sensors; that are known to fail causing problems. Is your car out of the vw factory warranty; if not you might have it checked out, check fir any recalls or if out, investing in a vw scan tool like the ross tech vcds, would be a good investment. This would enable you to read trouble codes and observe live data; which may reveal the problem?
You might try a hard reset and see, if this restores functionality to the top.
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