If a fault occurs that can be proven is directly related to the remap, you aren't covered by the VW warranty, and you need to go back to the tuner as it should be covered by their warranty.
Also while doing some data logging on a remapped car recently (mk4) an error popped up that I'd not seen before. It seems if your remap raises the factory set rev limiter the ECU logs every time you go over that limit, which according to VCDS may also void your warranty! (its possible that tuners can/are already coding into their maps a workaround to that little 'glitch' )