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The window regulator or plastic tabs attached to the glass is likely broken and will need to be replaced, if you can hear the motor running but the glass does not move. If you're handy with fixing cars, you can purchase a window regulator and change it out fairly easily by removing the door panel and swapping the regulator out. If the plastic tabs on the glass are broken, you will have to take it to an auto glass shop to have new tabs replaced on the glass.
I had this happen with a different vehicle. "My" issue was the security system. When I disconnected the wires going into the doors, it tripped the security system into the ignition lockout mode. I had to reset the computer (free and it only takes a few minutes). Mine was able to be reset with one of the code readers from O'Reilly Auto Parts which they will let you use for free. Some vehicles have a reset button built in. If you have a security system on your VW, first make sure all wires were reconnected and not broken during the installation of the doors. If everything checks out ok, then give your local VW dealer a call and ask to speak to someone in the service department. As the service person if there is a security system reset button anywhere on your car.
There may not be any other way to fix it except to replace your instrument panel. That's where your immobilizer is located. Or you could try this:
Try cold-booting the car. Remove both battery cables from the battery.
Short the battery cables together (away from the battery) for about 15
seconds. Reconnect the battery. No guarantees - I found this info at tdiclub.com.
remove the inside door trim and remove the weatherproof plastic that covers the holes in the door behind the trim.
You should have access to the door handle nuts and rods to remove the handle.
re assemble in the reverse order and make sure the weatherproof plastic is put back on and sealed or your door may let water enter the car via the door