Allow me to help you change the status of your paid invoices from Not Deposited to Deposited in QuickBooks Online (QBO).
When receiving payment in QuickBooks Online, if you chose to deposit the payments under the Undeposited funds account then this is the reason why the status of your invoice was showing as paid but not deposited.
To deposit these payments, here's how:
1. log in to your QuickBooks Online and click the Plus icon at the top.
2. Select Bank deposit under OTHER columns. Then, select the bank account you wish to deposit the payments in the Choose an account drop-down.
4. In the Received from, select the invoices by putting a checkmark on the box. Then, click Save and close.
You can use the screenshots below.
You can also use these handy articles for future reference about receiving invoice payment in QuickBooks Online: