Hello Thomas,
The issue of not able to remove App Engine domain mappings in case the domain is expired or not owned by the user seems like a known issue and a Feature Request is created in this regard with App Engine Engineering team. You can follow this link to track the progress of the Feature Request as App Engine Engineering team will provide update there.
As this Feature Request has suggested alternatively you can report this issue by creating a Public Issue or creating a case in case you have a support package and one of the Google Cloud Platform Support agent will assist you by notifying the issue to App Engine Engineering team internally to resolve it.
You can create a Public Issue by selecting “Create new App Engine issue” under Compute section. In case you need to share any personal or project specific information, please select the Private component of the App Engine issues.