Another question: I am atm copying all the files via SCP as I only want to duplicate them locally.
Personally I would have created one share added that to SMB, then under that share from windows create the folder structure as on your Raid 1, then copy files, this is much quicker than using WinSCP. Once you know you're OK before creating the second array, delete the SMB share then delete the shared folder, this is how I would approach it.