Messed up trying to upgrade drives, help!

Your procedure was the correct one.

I'd start by testing the two new drives in a Windows PC using Seatools.  I always start with the non-destructive full test, and follow up with the full write-zeros test.  That will take awhile (perhaps one day per drive) - but it will give some assurance that both disks are ok.   I have purchased some drives that passed one of these tests out of the box, but failed the other.  You can connect the drives with directly with SATA (assuming a desktop PC) or get a USB-SATA dock.

Assuming the drives pass, then boot up the NAS with only the 6 TB drive installed in slot 2.  Then hot-insert one of the (now blank) 12 TB drives in slot 1.  That should resync.

Once you are sure the resync has completed, you can then try hot-swapping drive 2 again.  

skwiggly wrote:

However, when powered back up, and accessed the web dashboard, I saw that the drives were now re-syncing, which I did not want since 12TB #2 had already synced.

Likely disk 1 was being resynced to disk 2.  Probably not an error, and interrupting that sync explains why disk 1 is now red.

One thing you should do for extra data safety is to connect the 6 TB drive from slot 1 to a PC and format it there.  Then copy your data to that drive over the network.  You have no redundancy at the moment, so any problems with drive 2 will result in data loss.