"can't restore all the files" message

I returned for a shoot to find that a couple of files that I had shot were not on the third of my four SXS cards. I know that I would not have deleted the files and there is definitely shot numbers that are missing on the cards. I remember when I switched from one of the cards to the other I got the "restore files on card A" which I executed. Then I had the message "some of the files cannot be restored." Am I missing a trick somewhere? I've got DVDs and access to tutorials, but they've never covered "hot swapping" or whatever. Do you know what I have done wrong in switching cards or is there another reason?

Any diagnosis gratefully received.

Yours

Mark