Thanks for reaching out, Matt. I'm here to make sure you'll get help as soon as possible.
Since this is related to API, I recommend reaching out to the Intuit Developer Community. They have the expertise and the right tools to investigate and fix the root cause of the missing document numbers from all your invoices. Here's how to contact them:
Moreover, once you're able to see the document numbers from all your invoices, you'll want to check this article for future reference on how to record invoice payments efficiently: Record invoice payments in QuickBooks Online.
Please leave a reply in this thread if you have questions or concerns within your invoices or with any QuickBooks Online products. We'll respond to you as soon as we can. Have a good one.
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