Similar problem experienced after updating my wife's iPhone to iOS 12.1.1. She's listens to audiobooks that she syncs from iTunes on her iMac. She's been following the same routine from early days with her iPods ... manually select audiobooks she wants to listen to, sync to her phone, listen to books, rinse, repeat. After updating to 12.1.1, on multiple instances she has finished listening to all tracks of an audio book and she goes back to her library [on her iPhone] to start a new book and all other books are gone. When she physically connects her iPhone to her iMac to re-sync with iTunes, all the missing audiobooks show as still selected in her iTunes:iPhone Sync Audiobooks list. look at "On My Device:Audiobook", all the expected books are shown as present on the device. But they're definitely not available from the iBooks.app on the iPhone. She tries to sync, and none of those books re-appear on her iPhone.
The only way we've been able to resync audiobooks is to disabled 'Sync Audiobooks' in iTunes, sync to clear audiobook selections entirely from the iPhone, re-enable 'Sync Audiobooks' and then sync again. All the selected audiobooks then show up back on her iPhone ... only to disappear again after she completes listening to an audiobook.
As noted above, she's never had this problem syncing and listening to audiobooks since first starting with iPods. This problem just started after upgrading her iPhone to 12.1.1. Her iPhone was previously running iOS 12.1.0.
[ reported as radar bug #46764078 ]