I fitted a new battery on my GTi yesterday.
It is fun & games, you have to use an OBD coder, Vagcom , OBDeleven for example.
You have to set the car to recognise the new battery, they obviously did that or the car will not start.
Straight away you will have a dashboard full of lights and various "bong" sounds, plus a handful of error codes pop up.
As you drive the car and some (not all) will disappear more or less instantly.
For the ACC & stop start, you have to drive for 5-10mins then clear the codes, it seems to think it has not got a correct signal or input from the system.
As I said, I did this, then cleared the codes, ACC & Stop start is back working fine.
I re-ran a scan and have the all clear with zero error codes shown.
It is a pain, but once you have cleared and got the car back to where it was, you should have no recurring issues.