If a school is administering CBT and giving the tests on the first two days of the CBT test window, does the school have to wait until the makeup period to administer makeup CBT sessions?

No, they do not. The school can choose to administer CBT makeup test sessions at any time after the school's/grade level's primary CBT administration is ended.

As soon as a CBT school has completed its regular two CBT sessions, the school may begin administering CBT makeup sessions anytime within the standard six-day CBT test window. The school may also decide to wait for the CBT makeup period. This is a local decision that can be determined by the district/school.