Hi,
I completed the remove operation.
As you mentioned the root certificate on the DC in both the Trusted Root Certificate and Trusted Intermediate Certificates will be removed.
The root certificates on the domain member in the Trusted Intermediate Certificates will be removed too, but certificate in the Trusted Root Certificate will be kept.(Only the first CA certificate will be kept, if you renewed the ca and have some renewed CA certificates , they will be removed.)
Best Regards,