I just tried using the manual cheque option on the pay vendors and it did not remove the invoice that I paid from the Pay Vendors window.  It did not remove it from the Vendors account either but did show up as a payment.

For the invoices that I pay online or do an intercompany transfer online I used to just pay by cheque.  I did use the option to pay by online banking and that worked so I decided to try it for manual cheque as well and it did not mark the invoice as paid.