Hindsight is 20:20, but for anyone else reading this, my method for server transfers like this is to have a physical offline backup from the start of the transfer process. (obviously would need more disks if you have a big array, but at this scale you should have enough experience to handle this)

Once I have the physical backup, I set it aside, unplugged, until the entire process is done and I confirm it all went well. Then I feel safe enough to use that drive angain after the first week or so goes smoothly.