This is a novel event, generally speaking, but Nintendo is broadly allowed to change the license on something they now wholly own. It'll be an interesting argument that can go either way — Nintendo is allowed to say they don't want anyone to distribute the code going forward that they own, but there was an explicit grant of license that may or may not survive the transfer of ownership.
Perhaps novel in terms that it resulted from a settlement, but not at all novel when it comes to license changes. Look at HashiCorp and Terraform that changed to a Business Source License. The community did not take kindly to the license switch and forked the last FOSS version licensed under MPL 2.0 by HashiCorp and it got picked up by the Linux Foundation (OpenTofu). Same thing happened with Redis when it ditched the BSD license for an SAL and an SSPL just a month ago, it's last published code under BSD was forked into a project known as Valkey, also adopted by the Linux Foundation and supported by a number of large players (AWS, Google Cloud, Oracle, etc..).
IANAL but to my understanding as long as the forks are from the last publicly available repo under GPL 3.0, a transfer of ownership to Nintendo does not cancel out the previous OSS nature of the code that was available, nor does it revoke the GPL 3.0 license, in fact GPL 3.0 is irrevocable as long as it's conditions are met. Nintendo would have recourse if they were to further develop that codebase and the forks were found to have incorporated the code developed under the new license into their versions, but that is not the case here. You cannot just rugpull GPL 3.0 because you own the code, everything published under GPL 3.0 remains under that license in perpetuity provided its conditions are being met.
