Missing music and books?

Recently all but one of my books in iBooks disappeared from my library.  Everything was backed up so I was able to restore it but last night I realized that all my music has disappeared as well.  I don't know for sure but suspect this happened at the same time which was Sunday. 
In both cases my material is backed up so I'll be able to restore it but it is still disconcerting that something like this happened.  Does anybody know of such a problem and the cause?  The cure? 
If it is a common problem is there a way to restore without manually dragging tracks back into the ipod? 
Thanks!

Well, yes. They're not completely lost, I know this. I have most of this material (songs and books) in my iTunes, and I can go and manually pick each one and add them again. But should this really be necessary? This way, I'll all the trouble of setting it up again, instead of just opening it how it last worked.
Although some files like pdfs that i saved either from an email, or saved from the web were located in iBooks and could be lost.
Recovering these files is only a part of the problem (which in most cases is easy to solve). The update erasing my whole music Library and bookshelf for no good reason is what bugs me and is a dissapointment with Apple.

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