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Welcome, @jboehmer. Glad to have you here.
Let's check your customer's profile to make sure both the invoices and payments are under their profile. Here's how:
If you're able to find a payment that isn't associated with an invoice and should be, here's how you can link it:
That's it! For more information on receiving payments, I recommend checking out: Record invoice payments in QuickBooks Online
Keep me up-to-date here by using the Reply option below. I'm here to ensure your continued success. Have a good one!