I see that your database is set-up for ACH payments, however this is only for ACH payments for Banks based on the United States. The best suggestion I can make for this scenerio would be to make a payment from one back to the other and then log the payment as a manual check, in Accounts Payable.
We do have an enhancements coming in the near future that will assist users with recording an ACH that occurred in the past. More to come on this in the coming weeks.
M3 Support Manager