A/P-B allows for entry of a manual check, but you would have to create a dummy vendor code for the purpose of entering voided checks.  A/P-B will ask you for the check number and you can enter the damaged check number so there is a record in the check register.  
 
However,   I am not sure if A/P-B will allow a manual check be entered for $0.  
Perhaps Alan or Lynn can help with this.