DaveFace
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DaveFace's post in Formatting encrypted drive without shutting down array was marked as the answerThe first instruction there is to stop the array, which is what I can't do. Unless I'm mistaken, stopping the array would re-encrypt the disks, and I am not 100% sure I can enter the correct passphrase again.
Edit:
In case anyone else finds themselves in this situation and unsure what to do, the passphrase is requested on start-up but stopping and starting the array afterwards does not require it to be entered again. Stopping the array will show the drives as 'encrypted' rather than 'encrypted and unlocked', but they will unlock. So you can reformat each drive and shift data around (e.g. using the unbalanced plugin) to recover it.
The lack of documentation about encryption is a bit frustrating when it carries this much risk.