To follow up for anyone who comes across it — it was relatively easy to copy over my Maildir-formatted folders. I just copied them into the appropriate location for Mailcow’s dovecot, made sure they were 5000:5000, and then for good measure did:
docker-compose exec dovecot-mailcow doveadm force-resync -u $username@$domain INBOX
After I was done, I did:
docker-compose exec dovecot-mailcow doveadm quota recalc -A
The encryption bit was a red herring, it functions fine with the old emails unencrypted.
In short, worked out fine for me.