The Ministry of Education's guidebook for foreign children says that if
you will leave Japan, including to return to another country, you should
consult the school or the municipal board of education before you go.
The page does not list a form, a deadline or a visa step. It does not
say what happens to a school place after you leave. Ask the school what
papers they need, and ask the board if a public-school place has to be
released. This article does not advise on residence status.
Your child's dates, not the general ones
Add your child and ward. The timeline does the rest.