Syncing from iTunes to iPad deletes content from iTunes

I recently bought three TV series to watch while going away for a few days. They downloaded fine to my iTunes Library and I synced them to my iPad. I watched them on my iPad through ATV2 and today I went back to the iTunes library only to find that none of the episodes in those tv series are physically in my library any more. Itunes thinks they are there but the files are actually missing. I still have them on my iPad.
Any ideas? I am going to be very annoyed if Apple claim I have to buy them again.

I managed to recover the files from the iPad by getting a piece of software to copy them from the iPad but this is far from ideal - is this going to happen again? Do I have to backup everytime I make a purchase just to be sure iTunes isn't going to decide to delete it?

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