I had my first crash at the library boss, so I had to test it haha. Seems to be working fine now, it respawns as expected. Since I can't reproduce it, I'm not sure what caused it to become unobtainable in my last playthrough
FYI I had the same bug happen to me, and I’m till in the “doesn’t appear but isn’t inventory” state. If it would be helpful I can dump my memory state or share my save files.