Can we restrict $0 payment in Positive pay file

Bank cannot validate the positive pay file when payment amount is $0. We have a scenario where Standard invoice amount is $100 and credit memo is $-100. When we submit the payment process, these two transactions will knock off and one payment record will be created with $0 amount.

Payment process will include multiple invoices payments along with the above $0 payment. All these payment records will be captured in POSPAY file including $0 payment and Bank has confirmed that validation can not be done for $0 payment, and minimum payment amount should be $0.

Please guide.