So you don't have any linked transaction? On your test did you have those? That is what keeps popping up, " This will remove any linked transactions. Do you want to keep your attachments?". When clicking YES, its back to an open invoice and all payments linked to this invoice are now gone. I have continued once after saving this and I won't do it again because it caused a huge mess in my reports, FOR 1 paid invoice being deleted. 

if you got the popup please just explain what you did after clicking YES to the above popup. How do you get that PAID invoice linked back with transactions and customer while showing up in PROJECTS and not charging the customer again? 

Thanks ZAC