Can someone with XY chromosomed answer a question?

As a gyno-American I never had to deal with a profound voice change, (though don't tell me women's voices don't encounter difficulties at puberty, particularly in the passaggio; all of a sudden, those runs that little coloraturas used to glide through, especially just above the staff? suddenly someone seems to have left their shoes on the stairs for you to trip over.)
Anyway, I have a boy in choir, he was a fine soprano until last year but often sang alto for me, both to stand near some other boys for butch camaraderie's sake, and because he had a GREAT EAR for harmony. That's an important point.
He could hold an interior part by himself.
If we sang something bluesy (this is not a liturgical choir,) he had no difficulty nailing the lowered third note of the scale and then, tuning it correctly to a major scale in the next measure.
Over the summer his voice changed, somewhat.
No cracking at all, and when we sing in unison he can just sing things in either octave. (He still has a very pretty voice above middle C, no straining, no loss of high notes yet.)
But he seem to have no sense of pitch in his "man's voice." He can no longer match pitches unless he is singing in the same octave as the girls.
Now I know even with adult men, who are not really experienced choristers, sometimes when passages are demonstrated by a woman's voice it is hard to "hear" which octave you are supposed to be singing in.
There are other changed voices in the group, and he can't match them on a harmony.
(I even brought an adult light baritone into rehearsal.)
He's 13 and I'm loathe to say anything even slightly critical, (up till last year, I had no problem correcting his rare mistakes, nor he in accepting criticism,) both because I know it's a sensitive age and I don't want him to become self-conscious, and because I don't want to say something that gives him incorrect notions of how a male voice should be produced.
And frankly, his baritone (I'm guessing that's where he'll end up,) is really nice, quite beautiful.
But he cannot sing a harmony, either on something he already knew, or something new and simple.
So my question is, is this normal?
Can someone with good intonation and a good ear, "lose" it when his voice changes?

Any male singers reading this, any information or advice gratefully accepted.

(I have a problem, my own fault, that rehearsal time is running short, and I excused him from a lot of early rehearsals, as I need to with most of the children because of their insane schedules. So the realization that he wasn't "catching up" instantly, which I expected of him, has put me in a bind...)