Firstly, name and shame your dealer!
Secondly, AFAIR, any modification to your car after its manufacture won't be covered by VW warranty. Any dealer modification (eg dealer-fitted ipod cable) comes with only a dealer warranty. Any problems due to "non-approved" modifications won't be covered by guarantee so they can turn round and say no.
As for the Connects2 thing, if it's causing problems with the HU, probably best to avoid it happening again and sell the cable (or keep it until your car is out of warranty), or get a new battery and keep it spare, or just don't go to the dealer next time it happens.