I was told by the dealer a week ago that my battery was flakey when I had it in for something else. Before I could replace it the charging light came on, and I limped home (barely) on the remaining juice while various systems started to shut down en route.

I've replaced the battery, but of course that didn't fix the charging light.

I'm advised not to drive the car for fear of voltage spikes damaging electronics. Apparently it's a bit of a job to even get at the alternator to assess the condition of the alternator/regulator. Now I'm looking at big $$$ to have the car towed and disassembled to even assess what needs to be done.

Has anyone had a similar issue with the 4.2l engine/Audi charging system???

 

in all likelihood it's your serpentine belt or the serpentine belt tensioner. We're talking about a $50 part or a $350 part (respectively) and a $500 job max if it's worst case - the tensioner.

The dealer is telling you not to do anything and trying to scare you so they can charge you a few hundred bucks for diagnosis, and then another $700 or so for the fix.

Your car is an 06. The Euro Addiction forum has a great B6/7 S4 section for deep tech questions like this one, so I would recommend posting this thread there to see what happens. You may have to register. There are a few S4 owners in Edmonton on the forum (on EA) and one of them may be able to come over and VAG-COM your car.