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Notification emails for receipts vs. invoices

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Trying to set up a reasonable solution for issuing invoices through Shopify (Plus). It looks like in order to accept partial payments for an outstanding order, I can't accept the payment on a Draft--a real order needs to be created first. But that triggers the Order Notification email, which is the same email that's sent as a receipt when a customer goes through regular checkout and pays on the spot. I can put tokens in the subject line, but I can't use Liquid conditionals to give us a different subject line for these two very different scenarios. Any recommendations?