Automatic resyncing does not apply to models 1990 thru early 95. It is unlikely you'll experience a problem with the top by changing the battery if the top is either fully up or stored when you do the change. I often disconnect my battery to work on audio or other accessories and I've never had a problem. If your top does develop a problem, do a forum search on soft top error codes for an explation on how to clear them. It's not too difficult and you should probably print out the procedure and keep it with your owner's manual.

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