Don't panic! This has happened to me with BoB a couple of times. Apparently one of the sites they link through to (I think it's the Mobipocket site) has a tendency to update their database without telling BoB, and all the links disappear until they're updated. If you write to BoB and tell them what's missing, they should be able to reinstate the books in your bookshelf.
But stripping off the DRM and making your own backup does seem like a sensible Plan B for future use.
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