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Just chiming in with a "me too" - I sync bookmarks with MobileMe, and I've noticed that when my MacBook tries to connect to a wireless network that has no Internet connectivity (eg: my ADSL router is still booting up), I end up losing the bookmarks on the MacBook. Then when it does get connectivity, it syncs the broken bookmarks with MobileMe, causing my other mac to lose the bookmarks too (I can watch it happen in real time).

I've found a temporary workaround is to quit OmniWeb on all computers (ahem... I should buy another licence, yes?), restore the backup on one computer. Then for each computer (starting with the one I've just restored bookmarks to): Start OmniWeb up, wait for the bookmarks to reappear, then quit OmniWeb.

If I leave OmniWeb running without bookmarks, it will helpfully delete the newly restored bookmarks when I quit the bookmarkless instance.

I'm now trying to replicate the exact conditions under which OmniWeb will delete my bookmarks.