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Have you tried fuses and checked if it has a power supply
it would appear that the it had a alternate power supply so it wasn't running thru the circuit breakers or relay. This must have been done by the bloke that fitted my alarm when the car was in the garage.
I found an inline fuse had blown. I replaced the fuse with another for it to blow again. I unplugged all window switches then plugged them all back in one by one until I found one that blew the fuse. Turns out both rear switches blew the fuses. Need new rear switches now.
I would look at it two ways , my choice would be put it back to how it was , if for some reason that’s a no , ? then what size fuse was in the in line fuse holder , electric windows use a lot of power , im thinking some where between 20 to 30 amps , the original fuse holder for the windows would say how much , if it was changed when the alarm was fitted was it intended to put all the windows up when locking , personally i don’t mind putting my own windows up , at least on the original old circuit there will be more fuses circuit protection correct tginkness of wires etc , how is it blowing when you use the rear windows are windows moving or fuse popping straight away , it may just be too much current rather than a window fault , some recourse from the garage ?