Hi,
This is SAP's standard functionality. Void Cheque option is basically for cancellation of entry (Due to any reason like Wrong Entry / Cheque Bounce / Want to issue new cheque or reason specified by you. ) In your case you already voided the said cheque (A) and issued new cheque (B). Now system will not allow you to again do the reversal of voiding effect. In this case you can change the cheque no. in Journal entry (Change the number as 'A' as this will help you to do the Bank Reconciliation. But change of Cheque No in Jornal Entry will not change the Cheque No. in Payment entry.
Regards,
Satish