I like testing out new themes from time to time, and I ran into a small problem the other day. My current theme only uses one sidebar for widgets. I tried out a theme with two sidebars, and I split my active widgets between the two sidebars. I decided that I didn't like the theme, and switched back to my single sidebar theme, only to notice that two of my widgets were missing!
It took me a while to realize what was going on, but sure enough, when I re-activated the theme with two sidebars and moved the widgets back to Sidebar 1, and switched to my old theme, everything was good again.