Hi there, @barlidge.

At this time, adding an existing invoice to a project will remove linked transactions. You can follow the steps shared by my colleague Rea_M above as an alternative.

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. But I want to let know that your voice matters and I'm submitting feedback directly to our engineers for consideration.

For now, you can visit our blog site so you'll be able to get the latest news about QuickBooks and what our Product Care Team is working on. 

Please keep in touch if there's anything else I can do to help you succeed with QuickBooks. I've got your back. Have a great day and be safe.