@Gautham G Thanks for reaching here!
You can migrate an active custom domain in Azure, between subscriptions or within the same subscription. However, such a migration without downtime requires the source app and the target app are assigned the same custom domain at a certain time.
Therefore, you need to make sure that the two apps aren't deployed to the same deployment unit (internally known as a webspace). A domain name can be assigned to only one app in each deployment unit.
You can find the deployment unit for your app by looking at the domain name of the FTP/S URL <deployment-unit>.ftp.azurewebsites.windows.net
.
Check and make sure the deployment unit is different between the source app and the target app.
The deployment unit of an app is determined by the App Service plan it's in. It's selected randomly by Azure when you create the plan and can't be changed. When you create two apps in the same resource group and the same region, Azure puts them in the same deployment unit.
However, there's no way to make sure that the opposite is true. In other words, the only way to create a plan in a different deployment unit is to keep creating a plan in a new resource group or region until you get a different deployment unit.
Suggest you to refer this detailed document here- Migrate an active DNS name to Azure App Service
Please let us know if further query or issue remains.