Create Invoices through Paypal Link

Welcome to the Community, Bendix.

When integrating third-party applications, QuickBooks Online (QBO) depends on the data sent by your third-party connector. In your case, I recommend reaching out to the PayTraQer Support Team to inquire whether they can modify the mapping of their account so that only the unlabeled paid invoices are synced to your QBO account. This adjustment will ensure that only the unpaid invoices are sent to QBO while excluding the payments.

You can check their contact information through the App information on the Find Apps page.

Here's how:

1. On the left panel, select Apps.
2. Choose the payment app you've integrated into your QBO account on the Overview page.
3. Scroll down till you see the Contact and Support information.

Additionally, you can refer to these helpful materials when you want to disconnect the apps you've installed or reposition the app ownership:

• Disconnect an app and change your subscription.
• Transfer app ownership or disconnect apps.

Don't hesitate to hit the reply button if you have other questions about managing your invoices through third-party applications in QBO, Bendix. The Community will assist you 24/7. Keep safe!

@Bendix 

Consider having a 3rd party gateway to generate your QBO invoice with the Paypal payment link. You don't need to use PayTraQer to reconcile the payment later.