We had AP checks print out of order with a zero dollar check print first. The rest of the 100+ checks were printed on plain paper. Without starting over accounting wants to delete the zero dollar check from the batch.
I am not aware of a way to delete after you have processed once. You can reprocess to get a new number sequence on the payments if you have had a print error. You also just reprint a portion of the checks if I remember correctly. You should have an Actions > Reprocess Payments options after the first process of the payments.
The fix for removing a check after the run has been printed was to make the check number 0 which made the check show pending in the batch and it could then be deleted.