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The "window drop" would not operate, by design, when the vehicle's battery drop below 9V, in order to preserve power for the starter. There is no way to bypass the automatic operation by any other means, physical or otherwise.
The good news is that the purpose of the window drop is just to be a able to clear the window seal lip. When you close the doors, just after they hit home and latch, the window pops up into the groove to create a better wind and rain seal, by driving the edge of the glass into the groove, nothing else.
The fact that it's set in place and not moving, due to a dead battery, does not cause any damage to the vehicle's window, door or anything else meaningful.
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