You're saying when you restart the device things disappear? Are the files still on disk after the restart?
Books can fail to show up for two reasons usually.
1) Failing memory. Any files do not show up, or the filesystem reverts back to a specific state after a reboot.
Failing memory is bad.
2) The indexer is jammed on a book with bad markup, and cannot add new books.
Solution: delete all the missing books, add one at a time until you track down the broken book.