When the warning appears, it usually gives you an option or a workaround to follow. Can you give a screenshot of the error?
Moreover, projects can be restored within 30 days before they are permanently deleted. A workaround is to restore the project, remove the custom domain on the restored project (as simple as clicking the trash button), and delete the project again. -- You received this message because you are subscribed to the Google Groups "Google App Engine" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/google-appengine. To view this discussion on the web visit https://groups.google.com/d/msgid/google-appengine/179d22d2-954b-4f05-ac5c-8914161832c5%40googlegroups.com. For more options, visit https://groups.google.com/d/optout.
