Hi there, @zolson.
If the status of an invoice will only show as deposited through QuickBooks payments, the payment has been posted into your bank.
Here are the different statuses of an invoice found in QuickBooks.
- Sent: You emailed the invoice to your customer
- Viewed: Your customer viewed the invoice. This includes any CC and BCC recipients of the email.
- Paid: Your customer paid the invoice in full (2-3 days for this to deposit in your bank account).
- Deposited: Your deposit should land in your bank a few business days after you were paid.
If the auto-apply credit feature is turned on, the credit will apply as payments to open invoices. We can turn it off by following the steps below:
- Click on the Gear icon.
- Select Account and Settings.
- In the Advanced section, select Automation.
- Unchecked the Automatically apply credits box.
- Click on Save.
As for the invoices that show deposited, let's delete the linked payments by going through the page. In the upper right corner of the screen, tap (Number) payment made (Amount), then click the Date of the pop-up.

This should answer your concern. I'm also including this article for additional information about received payments: How to record a customer payment.
I'm always around if there's anything else that I can help you with. Have a good day!