I have never once replied to the literal thousands of posts I've found in QB Support but I felt compelled to here due to the sheer frustration so many of you are experiencing. I can surely relate to the annoyances felt by all of you when you get stock responses by agents just trying to beef up their post count and not actually making an effort to even understand the situation much less provide actual help. 

Anyway! I wanted to say that I am a general manager for a firm who provides bookkeeping and accounting services to business across the country and I deal with this issue with so many of my clients. Two practical solutions to the system Intuit has designed are as follows:

1. If you choose to use sales receipts, I understand this is the preferred method of billing because you as the business owner have control over setting up those recurring payments so this option is most attractive. Card in hand, bill it, get the money! That being said, we end up with this exact problem and the only way to work around this is to check the report manually every month to ensure you've received the deposits you should have against your merchant account charges. 

2. You do have the option to set up recurring invoices. If you enable online payments in your invoice, you can then direct your customer to set up auto pay from the initial invoice. There are some sales concepts at play here which make this a less attractive option of course from the perspective of customer retention but it also makes the unpaid invoices factor much easier to detect than the sales receipt option. There's a video here which explains this: 

I wanted to specifically address the person who was saying that invoices are showing up as paid even though they haven't been. This issue is likely due to payments being received into undeposited funds erroneously or difficulties matching transactions in the bank feed correctly. These are both very common issues and I would suggest watching some videos found from the search terms: "undeposited funds" and "matching from the bank feed in QBO."

Finally, for the problem at hand when you know you have a sales receipt that's showing paid but hasn't been paid, the fix for this is to delete the sales receipt and recreate this as an invoice. If the amount is collectible, the amount lives in your AR as an asset until you receive the payment against your invoice. If the amount is uncollectable, you should create a credit memo (not vendor credit) for the amount of the invoice and categorize that amount to an expense account called "bad debt." Then go to "receive payment" and receive payment against that invoice with the credit memo you've created. This will remove the balance from AR and show the amount is a bad debt that is writing off the uncollectable amount. You can find more information about this if you search "how to write off an invoice in QuickBooks online."

Quickbooks is an incredibly user friendly program that takes sometimes complicated accounting principles and makes them effortless for the lay person to execute. This also has the effect of instilling a false sense of security when it comes to understanding of those principles and that's how we end up with lots of frustration and really messy books. I see this kind of think every day and it's unfortunate that the support professionals here aren't more tuned in to those circumstances. 

I hope I've provided some help! Good luck!