viper 5900 problem, 99 eclipse

Is the child safety lock on?

Did they check the 20A fuses to the 530t module itself? Do they know where that module was installed?

There is a (-) input connection and a ground-when-armed (-) connection to that module, and i'm not seeing how resetting the alarm brain (presumably by diconnecting the car battery) would affect these, and I'm not seeing why this would even affect door window switch operation/functionality. 

What kind of car do you have?

Is your car in the shop specifically for this reason? What are they repairing?

Why did they remove the battery?

Did the window system work flawlessly prior to you taking the car into the shop?

Could you give them your keyfob and determine if the keyfob works and if it re-initiates any window system?

it's really hard to say at this point what is going on.  I don't know if these guys are autobody guys/technicians/mechanics... but usually guys that do body work dont' necessarily do much alarm/aftermarket electronic work (some do, most don't). 

I'd first make sure the alarm was working, reset it if necessary and reprogram keyfobs if necessary.

Then,

I'd go through each fuse systematically, and work my way to the wiring, testing major wires with a voltmeter.  Then i'd inspect the window modules and the driver's door window switch module.

I'd also make sure separate fuse 12volt power lines that may have been snagged at the battery terminals (such as for the alarm brain or for the window modules) are still attached to the positive battery terminal