If the cheque has been cashed twice it is on the bank statement and needs to be entered in Sage 50. I would enter a prepayment in this vendors account using the same cheque number followed by 0xxxxDup. This gets the entry in Sage 50 so you can complete the bank reconciliation. When you receive the reimbursement for this amount enter a new pay later purchase invoice using the bank account number instead of an expense account on the detail line. Check the Record (Ctrl+J) to be certain your entry is a debit to the bank and a credit to  Accounts Payable. Once this is entered go to the Payments and open the vendor account. There should be two items waiting to be cleared, one positive and one negative. Change Payment by to Cash to prevent using another cheque number, then clear the matching amounts leaving a Zero balance to be paid. Post and you are done.