I have a similar issue with a twist. When I change the customer name to match the project name I get a message saying that all linked transactions will be removed. The only linked transaction is the estimate which I had converted into the invoice. If I click okay on that message box all of the line items get cleared and I'm left with a blank invoice.  At this point I back out of the screen without saving anything because I don't want to lose the info.

When the customer accepted the estimate I converted it an invoice, and also created the project. The two don't seem to be linked in any way. The customer has made a partial payment against the invoice but it hasn't updated in the project. 

What did I do wrong?

Thanks,

Sam