So far the only solution I have is to delete the books from my reader on the tablet and resend from Calibre. They now appear and have reappeared each time I connect to my tablet.
However, in correcting this I've noticed one thing. When searching for books on device it doesn't restrict itself to the folders you have specified.
Wouldn't it be more efficient/quicker only to search the folders you've specified instead of going through all my mp3's and films as well?