I have a FreeNAS setup with 4 1TB drives in a RAID10. With no more SATA ports on the motherboard, I want to upgrade this system to a RAID1 with 2 8TB drives. The majority of the data on the drives is user data although I also have a few FreeNAS VMs stored there as well as a few applications running in Jails and some snapshots.
Is there an optimal way to do this migration? Particularly in maintaining the structure that is necessary to FreeNAS (the VM locations, snapshots, etc).
Do you have a spare pci slot?
I do …
And listening 
I have one of these and it works in freenas. It’s cheap and will allow you to make a new pool out of the 2 8TB drives. Then do a clone via replication(zfs send, tom has a video on this).
https://www.amazon.com/puertos-tarjeta-controladora-no-Raid-SI-PEX40064/dp/B00AZ9T3OU
Thats a pretty tempting idea.
Will there be any issues switching the drives back to the motherboard SATA ports after?
Or is the performance/compatibility going to be so similar that its not worth it.
That card has a 2 lane PCI 2.0 interface so it will max out at 1GB per second, which is more than adequate. You can just leave it in there and use it or move the drives back to the motherboard sata ports if you wish.