This was a tremendous help. I was able to follow the steps almost exactly as you wrote them. The only except was that I had to change the estimate status back to pending. Apparently it goes to a closed status after it gets converted to an invoice, and as such I didn't get the button to convert it to a new invoice once I deleted the faulty invoice.  However as soon as I changed the estimate status back to pending the "convert to invoice" button reappeared and I followed the rest of the steps without a problem. 

Now my invoices are all linked to the applicable project and the world is right again. :)

Thanks!