The key is probably losing communication with the car part way through the sequence. That's one of the problems with the OEM remote setup, you have to keep the key depressed and sending/receiving a signal through the whole retraction sequence or it stops.
Put in a automatic roof mod gizmo like the Gaptech - then you just need to initiate the roof down (or up) sequence and it completes without further communication between the key and the car.
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