Hi Clinton, you are right. To be completely honest, Heidi and I "punted" on this because there are so many possible ways that people modify adapters and configuration that we worried that any formula we provided would end up messing up at least some people. In hindsight, though, we probably should have given some guidance on this point.
My personal experience is that upgrading is generally pretty straightforward. I always refer back to the basic install-by-hand instructions at http://www.asp.net/cssadapters/whitepaper.aspx#SamplesUsingInYourWebSite. If I follow these (replacing my older versions and adding new files as needed) things tend to work right away.
There have been very, very few cases where Heidi and I have changed CSS class names from one rev of the kit to another. For the most part this was simply because the classes didn't need to be changed. And, of course, we didn't want to "break" existing style sheets built up from the old names.
There have been changes in the successive revs of the kit, of course, but these tend to be highlighted in the readme or announcement docs. These generally involve support for additional controls or properties, etc. They don't uses break existing style sheets or involve hideous reconfiguring of your adapter code... happily.