UPDATE:
I destroyed the destination pool and recreated it, unlocked the encrypted filesystem and tried to do a recursive replication of the whole source pool. Once again, only the other unencrypted pool was copied to the destination. So, I setup a separate replication job just for the encrypted dataset, but when this is run, it finishes immediately, and no data is copied over. Here is the replication job page:
As you can see, the replication jobs for the encrypted filesystem took 0s and 1s. So something is preventing the encrypted filesystem from being replicated :/
The weird thing is that after running the replication job, the 'backup' pool shows unexpected data used values:
The values on the 'tank' pool and its filesystems correspond with the data stored in each one, but I don't know why 'backup' shows 2.03TB used.
UPDATE #2: I setup the same job without the 'recursive' option checked; I ran it and this time it looks like it is doing something (% progress is slowly updating). I will leave it running overnight and update this thread tomorrow with the results.