When you have chosen EU INVOICING METHOD under General settings -> Billing you expect that the Paid invoices will generate a separate numeration.
Such action is possible ONLY when you add transaction to the invoice.
Note: Changing invoice status manually to Paid doesn't tell HostBill that the invoice has been actually paid, so the system won't generate a separate numeration for such invoice.
When using manual transactions - like Bank Payment, please apply payments trough Invoice->Add Payment menu