I've found a couple of other threads with similar titles, but they don't seem to be about the same issue that I have.
When I edit or add a widget, sometimes one or more widgets that have been placed in the sidebar just disappear. It doesn't always happen, and I can't spot a pattern. I've had to start keeping a log of all the code and settings for every widget, as I often have to re-install them all.
I'm almost certain this is to do with running Widget Logic and PHP Code Widget plugins. I'm in the process of testing variations of deactivating and activating these, but I thought I'd see if anyone has encountered and maybe solved this?
The other hope is that the new widgets system in 2.8 might smooth things out...