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