AP Paycycle

Hello PS AP Gurus

I encountered a scenario as following

We ran ACH paycycle

Trial Register program  has total of (say) 1000 but the flat file for
ACH has a total  (say) 900 which is off
an amount paid to two vouchers (say 50 each). Both vouchers originally paid via
Payment Plus on previous day but I had the payment canceled and reissued to pay
as ACH instead.

Does trial register
consider all payment or FIN2025 program ignores cancel payment.

Thanks.

Gopal