DOES NOT WORK!

I have a customer who sent and invoice and it was paid. Now she wants it in a project. When I went to the invoice and selected the project, the invoice and payment are NOT linked. When I went to the payment and put the project in it, it created two separate transactions and the invoice still shows as unpaid. My only option is to delete the payment which is tied to Intuit payment transaction so now I cannot use the project feature for invoices that have been processed and paid. 

WHAT THE HELL?!!!

Not good. Not good at all. Please fix this or turn in your resignation. (Haha, kind of...)

Thanks.