I just installed Version 3.0 and copied a theme I've developed over the last few years into the Themes folder. When I moved from the Default theme to my theme it appeared to work okay with the exception of a few character entities from the upper-ASCII range. I edited those by hand and everything seems to work.
However, after I spent a lot of time adding widgets back into my theme and getting them looking the way I wanted, I switched to the Default theme and configured the widgets there the way I wanted. Imagine my surprise when I switched back to my theme and found that all the widgets were missing. They all got moved back to the Saved widgets area at the bottom of the screen. The second surprise was when I went back to the Default theme and found that all the widgets I had moved into it were also missing and back at the bottom of the screen.
There is no Update button on the Widgets screen so how do I get my changes to stick? This is a non-starter.