Chrome appears to have some fairly serious bugs that can lead to deleted bookmarks. I tried deleting a single bookmark in the bookmark manager, and it ended up deleting an entire folder. Fortunately, there is a Bookmarks.bak available until the next time you quit chrome. This wouldn’t have been such a big problem if I hadn’t already been fighting bugs with the Xmarks bookmark syncing plugin for Chrome. I have now turned on Chrome’s built-in bookmark syncing, but I still use Firefox quite a bit, so I wish Xmarks and Chrome weren’t so buggy. This is why I normally avoid beta software like the plague.

http://www.google.com/support/forum/p/Chrome/thread?tid=56d0b36c2e503bd6&hl=en