After battery died now the top doesn't retract

I didn't drive my boxster for 2 1/2 weeks while away for holidays and no I didn't know about the trickle charger. My battery died and I had to get the key out of the remore to open the car door.  I had to jump start the car door and the fuse panel in order to open up the hood.  Called AAA he jump started the car and I drove it for 30 minutes to charge up the battery.  The next day it didn't start again and I was warned that I might need to replace the battery.  I called AAA again to jump start the car but the tech told me that it was a loose connection after he tighten it, the car started.  I then tried to put the top down but it said it is opening but not in final position.  I went to 2 separate Porsche tech/shop that my friends recommended but they don't know what's wrong except it is some communication issue.  The convertiable motors don't know what positon they are in.  Please help!