Which is faster: Encrypt empty external disk or leave data on disk while encrypting
Leave the data on the disk being encrypted to achieve the fastest speed.

Full-disk encryption encrypts the entire disk, no matter what data is or isn’t there. Otherwise an adversary could easily determine which sections were blank, and attack only the ones that weren’t all 0s.

That’s one weakness of per-file encryption: allowing an attacker to determine what they want to target.

The way you chose to perform this operation, your empty disk will be fully encrypted once. Then once you move the 1 TB back onto it, encryption will be performed a second time on half of your drive.

This means it will have taken 50% longer to encrypt the drive vs. if you had left the files on the drive to begin with. Then add to that the amount of time required to shuffle the data back and forth, and you end up with a significant time loss.

Now since the process has already started, it’s more advantageous to let it complete before moving the files back over. Spinning hard drives really struggle with writing multiple areas of a drive at a time (which would occur if you encrypt one area while copying files to another).

If the external is an SSD, copying while the initial encryption takes place might not impact the process as much.