It seems that you have been affected by a known issue and currently the App Engine engineering team is working on a fix but there is no ETA at the moment.
Currently, there are two potential workarounds for this issue :
1. Run the following gcloud command to add a custom domain to your application:
gcloud app domain-mappings create DOMAIN
2. Use the app.domainMappings.create API method in the Admin API.
You may find more information regarding this by reviewing step 4 of the following article.
However, if the aforementioned workarounds didn’t help you to resolve the issue please open a private issue on Issue Tracker with providing the output of gcloud command mentioned above with the verbosity flag set to DEBUG as this will help us to narrow down and inspect the issue further.
Thanks for your understanding.