Hello there,
I understand how important to be able to correctly add your transactions to a specific project in QuickBooks Online. At this time the system does not allow to automatically apply existing invoice that has a linked payment or credit to be linked to a project.
I can understand how helpful it is to be able to automatically add transactions to a project without re-applying the payment or credit to the invoice. I've added this to our report and let our Product Development team know about the project feature offered.
For more details about using the project feature in QuickBooks Online, please check this link Set up and create projects in QuickBooks Online.
Feel free to post again in the Community if you have more questions.
