Not sure I understand the question.
–If your D can’t take a class because she wasn’t approved to take that level of rigor course by the HS then I would not mention it. (I don’t think this is the case)
–If your D was approved to take a class and could not take it due to a scheduling conflict I’d ask that it be noted in the LOR.
–I’d hope the guidance counselor would take scheduling conflicts into account when determining the overall level of course rigor box that gets checked on his/her LOR.