Some books are specific to the type of Nook - does the Book you searched for have versions for Nook HD/HD+ and Nook color? You could check this out on the internet Nook store..
The other thing is, books sideloaded to your SD card may appear in 'My Files'>Books rather than the Books section of the library. When you look at My Files, see if there is an option at the top to change to SD card to see the books on there.
If your books are HD/HD+ compatible & all Nook books that you can't see, it may be worth contacting the very helpful Alex the Moderator of this forum to see what he can do to help.
The other thing that has affected peoples' books is passing their other device on to a friend or family member who unknowingly deletes books from the NC which also deletes it from your HD/HD+.....