Thanks everyone.
@PoutineLover, yes, I think a letter of explanation is a good idea and we'll probably do that.
@historienne, it was a mixture. His first schools were the local public schools and the second school is a private IB school. So the two schools have very different requirements and classes. But in general, in both 10th grade years, he did take English, chemistry, and math which could be considered retakes. The other half of his schedule was different.
@madamwitty, I don't know. He is planning to apply a year from now in the fall of his senior year, so my guess was that they would want to see 9th through 11th grade grades. The new school would only have his 10th and 11th grades. I can see some schools not even admitting him if he doesn't provide all high school transcripts because they could consider his application to be incomplete.
I was hoping for a general answer, but he's likely only to apply to 3-4 schools, so we're probably better off just calling each school individually as some of you suggested.
Thanks!!