It shouldn't have shorted the circuit. When I was parting out a x5 I used a portable battery jumper to roll the all my windows up/down using spade terminals plugged in directly to the motor and just switching polarities to move them up/down.
The terminals are very close to each other on the motor so if I wasn't careful it would spark but it wouldn't make them stop functioning. Didn't even blow a fuse.
I would check your window switches.
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2005 Imola 4.8iS
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