Same issue. One minute they were there then the next they were gone in the Books iOS app. (iPhone 8, iOS 12.1.1) I had recently downloaded an audiobook from the Book store but that may be coincidental. iTunes showed the manually-transferred audiobooks as still present on my iPhone.
I suspected a corrupt data file for the Books app was preventing the app showing these files. The fix for me was the nuclear option of switching from "manually manage music and video" to "sync selected audiobooks" in iTunes, erasing all manually transferred info and files and replacing it with whatever is selected in iTunes sync settings. (*** If you have a lot of manually transferred music, movies, TV shows, etc, switching to "Sync Audiobooks" will delete all these items from your iPhone! *** I only did this after adding all my manually transferred music to a new "iPhone Music" playlist in iTunes to re-transfer later. I didn't have manually transferred movies, TV shows, etc to worry about—only audiobooks and music.)
Syncing audiobooks with iTunes seems to have fixed the issue. I guess changing to "sync all/selected audiobooks" in iTunes deleted the corrupted data file and solved the problem. Switching back to "manually manage music and videos" and my audiobooks are all still available in the Books app.
I hope this helps.
