If the custom domain in your CNAME file is already used by another GitHub Pages site, you will receive a page build warning. A custom domain in a CNAME file can only be used once. Here are some examples of when you'll receive a page build warning for a duplicate custom domain:
If you have an an apex domain such as example.com in your CNAME file, this means that either example.com or its www subdomain (www.example.com) has been used in a CNAME file in another repository and is being used by the corresponding GitHub Pages site.
Likewise, if you have a www subdomain such as www.example.com in your CNAME file, this means that either www.example.com or its apex domain (example.com) has been used in a CNAME file in another repository and is being used by the corresponding GitHub Pages site.
参见官网的说明。
就是说,只有第一个项目是有效的。