I have zones owned by the root user in WHM. How can we migrate those zones to the new server?
Unfortunately, cPanel Transfer tools can only migrate DNS zones that are associated with cPanel accounts. If zones have been created manually as the root user or in WHM as root, these zones will need to be transferred to the new server manually. It is best to create an account to host these zones which will make it easier to transfer zones in the future. The main thing you want to avoid for transfer purposes is having data not associated with cPanel accounts. Ensuring all data is associated with cPanel accounts in some manner will make it easier to migrate between servers.
Additionally, if a zone is missing you can write this zone between servers via DNS Clustering.
For example, establish the DNS cluster relationship between affected servers. Then sync the zone to copy it between servers.