The soft top control module should reset every time the ignition switch is off and the key is pulled out. There are two types of flashes. If the switch flashes fast it means the luggage cover in the trunk is not in place. If the light flashes slow it means there is an electrical problem. Meaning the control module is not seeing one of the micro-switches in the correct position. You can try manually opening and closing the soft top by locating the pressure relief screw in the back of the trunk. There will be a little flap of carpet towards the left center. Use a flat blade screwdriver to turn the bleeder screw to the left. This allows the hydraulic fluid to bypass the pump so that the top can be moved manually. You will need a 5mm allen to unlock/lock the latches.. Double check in the owners manual there might be illustrations I can't remember for sure if it does or doesn't.
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