The very last page of Bleach #668 gives a few clues.
Yachiru suddenly appears out of nowhere and says to Kenpachi:
Silly goose, if you would just use me properly, there wouldn't be anyone you wouldn't be able to cut down.
She then touches him, which causes:
him to get a power boost, which he wonders about.
She ends the exchange with explaining to him:
That power is what everyone's been calling "Bankai".
All of these suggest the following:
Yachiru is Kenpachi's Bankai. He is unable to call out his Bankai anymore (he was never able to, consciously - the original appearance may have happened subconsciously), therefore, Yachiru is gone.
Yachiru is his Zanpaktou spirit, again, one he has never been able to consciously communicate with. Though, I can't explain her disappearance if that were the case.