Migrating Subdomains from Plesk

I have a bunch of subdomains that need to be migrated from Plesk to cPanel but the transfer tool only sees the root domain. I had to manually create the root domain on the server and it's tied in with the hostname and nameservers. So I need to move these subdomains over but can't delete the main domain to do it. The transfer tool shows this as a domain conflict because it already exists on the server. Are there any other options besides manually moving all these sites?