He’ll never know it was gone. Yes, he will. How? He’ll just know. Well, he’s never noticed before. Maybe he’ll notice now.
I had an idea for a prompt after rewatching Hell Sent: What if there was an AU version where the Doctor has to return to the TARDIS after Clara's death to tell their child(ren). Like he doesn't know how to explain, and he checks the prompt cards, but can't find anything, and has to try an explain it the best he can.