Some court precedents regarding the return of children are listed in INCADAT, the database of the Hague Conference on Private International Law.
If you are interested, please refer to it.
Here is an overview of recent court precedents regarding publicly available discussions.

Of these, ３ are Supreme Court decisions.

・The Supreme Court First Petty Bench decision, March 15 2018(Grounds Non-Convention issues; Habeas Corpus )

Child return was ordered and indirect enforcement failed due to the mother’s strenuous resistance and the child’s objection. The father filed a request for habeas corpus relief.

The Supreme Court ruled that there are special circumstances in which a mature child cannot be seen to be staying with the taking parent based on his free will, so continued care of the child in defiance of a return order can amount to “restraint” under the Habeas Corpus Act and Habeas Corpus Rules. The continued “restraint” by the taking parent in breach of a return order is regardes as “conspicuously illegal”. Therefore, the Supreme Court ruled that the requirements of a habeas corpus order are satisfied. 

・The Supreme Court First Petty Bench decision, December 21 2017(Grounds Objections of the Child to a Return)

This is the only Supreme Court decision in Japan that modified a final and binding return order based on a change in circumstances, underArt.117(1) of  the Hague Convention Implementation Act.

Four children (two sets of twins), previously living in the U.S. and wrongfully retained in Japan, were initially ordered to be returned in January 2016.

However, the Osaka High Court amended the order, citing changes in the children's situation.

The Supreme Court upheld this modification and denied the father's petition to enforce the original return order.

・Supreme Court First Petty Bench Decision April 16, 2020

The Supreme Court concluded that the return clause reached in conciliation can, upon the party’s request, be modified pursuant to Art 117(1) Implementation Act mutatis mutandis. The Justices quashed the lower instance decision and remanded the case to the Tokyo High Court for further examination.