My kindle seems to have "lost" all of its books overnight! I have been able to find the downloaded ones in my Kindle library but no others. Calibre claims all of my books and documents are on the kindle but I cannot see any of them. I wonder if anyone can help me with this problem.
Not sure this will help but ... This happened to me and I had to update the firmware in my (older model) kindle so that it could recognize azw3 books.
Check the file extension of the books not being recognized. If they are azw3, then update the firmware. If they are mobi, then try converting one to azw3 using Calibre and re-load. If that works then use Calibre to convert the rest.