Hello there,

I appreciate your interest in linking your invoices to the projects you've made. I'm here to clarify things about these features.

I can see how seamless your work will be if the linked transactions won't be removed when adding it to an existing invoice to a project. However, this is currently unavailable in the program. This is because the Project feature does not support linking multiple customer invoices under one Project. 

The invoice was also linked to the customer, that's why it'll be removed once you link it to a project. To fix this, you can delete the invoice and link the Quote to the project.
 

1. Go to the Sales menu and select the Invoices tab.
2. Locate the invoice, click the drop-down arrow under the Actions column, then select Delete.
3. Go to the All Sales tab, then find the Quote. You can select the Filter drop-down to easily locate the transaction.
4. Double-click the quote, then select the project name under the Customer name section.
5. Click Save.

Once done, you can now create an invoice out of the quote. Just select the Create invoice button, then save. I've attached a screenshot below for your reference.

If you want to link multiple invoices to a project, you'll want to consider creating a project as a sub customer. It only allow transactions to be posted under that one name. If you already have existing invoices that you wish to attach under a new project you can do so by:

1. Go to the Sales menu and select the Invoices tab.
2. Select Customer drop down field, click the Project name.
3. Tap Save & Close.

This will then change the invoice assigned from one customer to the sub-customer which is the project you have created, which will then appear under the projects transactions in the Project tab. 
 

For additional reference about the project feature, check out this article: Set up and use the Projects feature.

If you have more questions about projects or other concerns with QuickBooks Online, please let me know in your reply. I'll be around to help you some more.