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That's why I asked if the doors are closed. It has happened to quite a few people. They leave the door(s) open while working on the car, the battery dies then they can't get the top up because the windows aren't indexed and they can't index the windows because they are trying to do it with the door(s) open.
My recommendation is, with the battery charged or replaced, get in, close the doors then re-index the windows then the top will work.
St. Jude Donor '08-'09-'10-'11-'12-'13-'14-'15-'16
Happened to me
I had disconnected the battery on my 07 vert. When I went to re-index the windows, the passenger side worked, not the drivers side.
I had to close the door with the engine running to allow the window to operate. Don't ask me where they came up with this sequence, but, the window only worked after I closed the door!
ok windows work, top did work. to test I put it down and then back up. but the body cover would not come back down. I released the pressure on the hex nut power top but the body part is still up in the air and won't move.