Change customer and invoicee of duplicate account's paid order to correct non-duplicate user.
Refund to account credit (and check the cancel membership checkbox). This will refund the amount to the correct user's account credit.
Pay for the outstanding order on the correct user's account with account credit.
Cancel the subscription on the duplicate user's account (with the reason in the dropdown set to "Duplicate Subscription").
Don't update the recipient on the order or subscription.
There will still be a cancelled membership on the duplicate user's account- we aren't able to delete that currently. As long as you choose the "Duplicate subscription" reason when cancelling the subscription on the duplicate user, the cancelled membership won't be counted in reports of cancelled members.