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My name is ***** ***** I am a professional here at Just Answer. I noticed that your question had not received a response and thought I would see if you still need help with this.I apologize for the delay and I hope I can still assist you with this here.
This can be a fault with a roof position switch/micro switch causing this issue here.I have seen micro switch failure in the past before cause issues like this here with the affected micro switch needing replaced.When the top locks usually the latch micro switch sends a signal that the top is secured.If this switch has failed to do this (as it may need replaced as this is most common) this fault here can occur.
You will need to have the micro switch signals checked using a compatible scan tool or dealers sds machine that can communicate with the roof control unit to locate if and which micro switch is at fault needing replaced.This sounds to be a fault with the final lock/latch switch itself needing replaced but this will need checked to locate which is the cause here for sure.
This can disable the windows from rolling up manually in some cases as the roof control unit doesnt know what position the roof is in as well as affect the windows from rolling up once the top is secured.
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