Strange camshaft noises, longterm issues

[Jon/Audi A4]

My 2001 1.8t A4 is going in for one of its last service visits on tuesday.  
I had the head tech at the local dealership listen to the engine running 
at idle and he thought it was best to bring it in ASAP (I only have 1200 
miles remaining on the warranty), instead of waiting for the final 50k 
service.

Anyway, there has been a rattle from the engine bay for some time.  I was 
originally told it was the heat shield rattling against my exhaust for 
some reason.  They couldn't find where it was actually touching, rubbing, 
etc.  So I ~ignored~ it.  This was practically 20k miles ago.  Fast 
forward to 47k miles, the noise is now *MUCH* louder and occurs more 
often.  Recently, I had a Check Engine Light (CEL) come on.  I looked at 
it with VAG-COM and cleared the code. The code was:

16395  P0020  -A- Camshaft Pos. Actuator Circ. Bank 2 Malfunction 
(intermittent)

A week later, I checked the fault codes again and I had the same code, 
plus this one:

17939  P1531  Camshaft Control Circuit ope

Now, my question to the list, since the dealership will be taking care of 
this under warranty:  Are there any long term affects of running my car 
with this ~problem~ for 20k+ miles?  FYI: never before did it "throw a 
code" or cause a CEL.  

I have taken good care of the car to this point and would really like to 
squeeze 100k+ miles out of her, and besides that, I love the car.

Thanks.

Jon