I have a 2001 996 C4 Cab . I let the battery go flat after the car had been standing for a few weeks. I had installed a new battery only a few weeks beforehand. I knew there was a fair chance it would go flat so had left the bonnet latch open so could get to the battery to jump start it and managed to get it going ok. However when I powered the drivers side window down , I couldn't get it up again. I took the car for a 30 minute drive but it would not reset the drivers window. I put the car on charge to let the battery upto to full charge. I had the hard top on and seemed to recall that I'd had windows out of synch previously and operating the hood a couple of times got them working again. So a couple of days later i removed the hard top and operated the hood. First time the passenger window went down and and came back up again when the hood came back up, but the driver window didn't move (still fully down) . I did it again but this time when the hood came up the pass window stayed down . I operated it a few more times but neither windows are now coming up . Any ideas appreciated.

 

From your symptoms (battery drain and window function) you have a malfunction of the alarm control unit (located under the drivers seat).

Remove the drivers seat, or position it so that you can access the alarm control unit. Remove the alarm control and open it up and inspect for corrosion. It is very common to get corrosion in them if any drains are clogged and the carpet becomes wet ( a lot of the times unknown to the operator).

There are lots of threads with instructions on how to do this, and to clean and verify the drains.

 

Is this the same as replacing an "alarm control unit that has corrosion from a flood caused by clogged drain?" https://www.ecudoctors.com/products/...-plug-and-play

It seems this fix needs me to send in keys and my ECU?! still looking for more threads on this...

 

You can get lucky and just get the unit out of the car, and make sure its dried out..
Clean the connectors and reinstall, its a cheap test..

Disconnect the battery BEFORE you disconnect the security module.
its possible your module is just confused from the dead battery incident.
They don't like their mother ship disappearing on them.