The convertible top on my car is stuck partially open. I also can't open the trunk, and the rear window is opening backwards.
There is a technical service bulletin from Volkswagen for updated programming to remedy inconsistent operation of the convertible top; you may want to take your Eos to a dealer to get the update. Also, disconnecting the battery for 15 minutes, then reconnecting it, could restore operation. There is also an emergency closing procedure that is outlined in the owner’s manual.
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