The MS classes do count toward the verified credits in APS. You have to accept the grade in that class to count the SOL.
We initially, when he took the classes, opted to keep all DS's MS credits. It was a mix of As and Bs and I anticipated that would also be what he'd get in HS so wasn't too concerned about it impacting his GPA. He became a much better student in HS, all As 2nd half of 10th, all 11th and wanted to drop the MS B grades. When we reviewed DS's transcript with his counselor in 11th, we learned that he could drop one of them but not the other because that one was counting as a verified credit and he did not now have an opportunity to take another SOL to meet that verified credit need. He'd have had to take an SOL in one of his 9th grade classes but didn't because at that point he didn't need to.