@lala516 if I understand correctly …
I think the intent is to list only the new private school as “attended for 9-12”, which you hope would, at college application time in 3 years, result in no grades being requested from the previous 9th-10th grade school. The newly-discovered problem is that if, in January 2022, the student starts 2nd semester of the new 9th grade year, the school will have no grades to enter for the 1st semester of the new 9th grade year.
Assuming the new school has no plans to “transfer” your son’s 3 semesters of grades (all of 9th and 1st semester of 10th grade) into their grading system, and that the new school plans to allow your son to progress to the 10th grade in August 2022 with only one semester of 9th grade schooling on their books, I suggest you list only the grades the new school will record for 9th grade, which will be only the 2nd semester of 9th grade.
Keep in mind this may put your son behind in having enough credits to graduate, but you can address that by maybe taking summer school classes, etc, over the next 3.5 years.