This morning I finally let Firefox 3.x upgrade to 3.0.4 after it bugging me to do it the past 4 days. As a reward Firefox deleted some of my bookmarks and duplicated others. So I tried to clear the bookmarks and import from a saved HTML file: quell surprise, you can't delete all bookmarks at once, you have to manually delete them a folder at a time. The only person stupider than the engineers at Mozilla are me for continuing to use the product.
The bookmark system is a pain but otherwise I don't know what you're on about. FF3 is a great browser (comparatively anyway).
What I'm on about is that it's going to take me 1-2 hours to a) delete the current horked bookmarks, and b) get my old bookmarks re-installed.
my dad has the same problem. he's always complaining about updates clearing his bookmarks or somehow messing them up. but i've been using firefox since v0.9 on various computers and operating systems and it has never once happened to me. i guess some people are just unlucky with it.
I have about 150 bookmarks between professional and personal use, and haven't experienced any loss. (I really shouldn't have said that should I? ) I use Foxmarks to synchronize my bookmarks between my work destop, laptop, and personal desktop. Perhaps using something like that can protect you from these issues.