I don't know the exact answer about the warranty situation, but I would have thought that surely it would extend the warranty to the date of the parts, or in this case wheels, were replaced.
I had to have mine refurbished back in March this year, and the company who done them gave me a new warranty for 1 year (providing the damage isn't caused by me - such as kerbing).
I was told when I went to by a new set of wheels on my previous car that I need to wash them every time I make a drive in the winter due to salt - just a simple rinse to get rid of the salt clinging to the lacquer.
British chrome alloys had the same problem when they were first released over here, because of the finish they corroded pretty bad.
Just keep washing them, and give them an occasional high polymer protectant to create a barrier between the lacquer and anything such as brake dust/salt clinging.