TLDR: you can not set up autopay on existing recurring transactions. I am partially posting so that others are aware and partially because I would like to turn off the option for autopay for some customers to prevent the issues I'm having now. Is that possible?

This all started when a customer set up recurring payments, but they weren't withdrawn as they should have been. Neither I nor the customer was alerted of the issue. 

This help article says, "If you already have a recurring invoice setup, you don’t need to create a new one.

Important: You can edit ‌recurring templates with Autopay setup. If you change any of these fields, Autopay will be canceled..."

However, after a 3 hour chat with QBO support and backend support I was advised, "Setting upa payment method to a old recurring invoice can process one timepayment and that will be the date the customer authorized andsetup. But, it does not mean that after they setup autopay it will gothrough on the next month as the recurring invoice got affected tothe changes. They suggest that when a customer wants to setup anautopay merchant should cancel or create a new recurring invoicetemplate and then let their client to enroll to autopay. That way,payments will be processed on the setup date and invoice willnever encounter issue."

To make sure I was understanding correctly, I asked, "are you saying every time someone sets up autopay, I have to cancel their recurring invoice and cancel their autopay. Then create a new recurring invoice, and have them set up recurring payments again?" The answer was "yes" that is what they are saying. 

The capabilities of autopay and recurring transactions are being misrepresented in the help article and the website. Not only is it not saving me time, it's creating even more work and frustrating my customers.