Did they account for inter-state relocation? Send the children to live with grandparents or aunt/uncle who is in a state where the schools did not close or where they could go to a low-cost private school that did not close.
For such a lengthy article, it was surprisingly limited in it’s scope.
What you just described was apparently not even considered as a likely factor in the reduced enrollment.
The article was about 3X longer than it had to be and tended to repeat its own message a couple of times.
Yes, they are saying these kids are not accounted for anywhere in system.