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Greetings, @bwg. It's a pleasure to see you here in the Community.
Let me provide you with some additional information about recovering deleted invoices in QuickBooks Online (QBO).
The existing invoice was originally linked to the customer and not to the project. 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.
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.
You can use the "job costing" feature to calculate your profits and cost by the project. If you wish to track your project labor costs, calculate the hourly cost rate for each worker. For the detailed steps, you can check out Step 5: Track your hourly time costs section of this article: Track income, costs, and profitability by the project.
You can refer to this article for the step-by-step process on how to add paid invoices to a project: Add existing invoices to QuickBooks Online Projects.
Keep us posted on how your call goes by leaving a comment below. I'm always here to help. Stay safe always.