I have a 2001 Passat GLS V6 4Motion which has developed transmission
shift problems.

The drain holes in the sunroof became clogged and I ended up with water
under the rear passenger seat. I fixed the drain problem and dried up
the water, but in doing so I mistakenly left the ignition switch in the
open position when I had the sunroof open to dry things out. The
battery discharged and I had to recharge it. I also took the battery
out to check the drain hole under the battery.

I think I have to take the car to the dealer to reflash the TCM. The
problem seems intermittent and does not always go into the limp mode
(all gear lights lite and defaults to 3rd gear only).

Has anyone had similar problems and how much can I expect the dealer to
charge for resetting the TCM?

Thanks