Prepayment invoice showing wrong status as cancelled

Hi Guru's

                  I have a Issue with Prepayment invoice, where the prepayment Invoice was fully paid in 2 cheques. Now out of those 2 cheques, one cheque got voided & user has cancelled the Invoice. now the Prepayment Invoice is partly paid but now in cancelled status which is wrong. Please advise.

I.e  Say Example :-  Prepayment invoice (worth 2000)  was paid in multiple cheques (i.e 1000 & 1000). now one cheque got voided but now the status of prepayment which is partly paid as 1000 is cancelled status. Please advise