Shooting Free Throw on wrong end

[Jimgolf]

I was working the clock at a CYO (NHFS Rules) game two weeks ago and ran into this situation: Two man, second man arrives 1 minutes into game (no parking in area). Late official calls foul, two shots for visiting team, has shooter take shot at wrong basket, shot made. Scorer's table gets officials' attention, tells them they're shooting at wrong basket. Ref tells scorer to count basket, administers second shot at correct basket. I tell him that I think first shot shouldn't be counted (Rule 2). He says no. Other ref doesn't get involved in discussion. Game goes on, ends in tie, home team loses in overtime.

Later, I go over the NFHS rule book, re-read 2-10. It seems to me ref was incorrect. Run into this ref this past Sunday, ask him about it after the game, also get a more senior ref involved in discussion. They seem unsure of the correct resolution for this situation, but state that ref ruled correctly. Senior ref promises to at least check rule book (not a bad thing to carry with you in your bag).

Was ref correct, or should first free throw been re-shot at correct basket? By the way, in 37 years of playing, coaching, reffing, scoring, timekeeping, spectating, I have never seen this happen before.