I have used the Bookmarks Bar for years for my main site to keep bookmarks that I use. The sidebar is far less frequently accessed. Over the past week, entire folders are disappearing from bookmarks bar, taking countless sites that I use. I updated Safari recently to 5.1.2, and security update. I am running OS X 10.6.8. I booted from an external drive with SuperDuper, backed up a few days ago, but it was missing the folders. These bookmark folders have been stable for years (as a system).
Do you have iCloud turn-on for your bookmarks? I did and found horrendous anomalies with my bookmark folders between my iMac, MacBook Pro, iPhone, and iPad. I could not get the issue solved and so far no solutions for it. My only recurse was to turn off iCloud/Bookmarks and restore my original bookmarks from backup and sync with iTunes. That solved my problem.