Anti-theft system won't turn off after replacing car window

The driver's side window on our 1999 VW Passat 4 door sedan (62,000 miles) was shattered by a rock from a passing car. After the auto glass technician replaced the window, the car won't start. When we turn the key, the dashboard indicator lights, fans, radio, etc. Come on, but nothing else happens. The battery is fully charged. The indicator light near the door lock that tells us the anti-theft system is engaged continues to flash and will not turn off, either with the key or the remote control. The locks and windows work, but the dome lights do not. We think the anti-theft system was somehow affected by the work on the window. Is this possible? Is there a way to disable or reset it? The auto glass technicians don't seem to have any ideas.