A server administrator may have made a decision at some point to add DNS zones using "Add a DNS Zone" in WHM and later decided to move those domains so they are instead associated with a cPanel user.
This requires manual file changes in /var/cpanel/users/ so it is recommended to first make a copy by doing
cp -ax /var/cpanel/users/ /var/cpanel/users.$(date +%s)
Next, the system user configuration file needs to be modified to remove the DNS zone added. The file to modify is
and in this file, there will be DNS lines that are incremented like this
The domains that need to be move must be removed from here.
Next, the cPanel account that will have the domain's association needs to be modified in the same location. Let's say the cPanel user is cpuser then modify /var/cpanel/users/cpuser and add DNS lines with the domains that were removed. You will need to check what was the last incremental number was and create a DNS line with the next one needed.
After the domains are added to the desired cPanel users the following would need to be run to complete the association.