Hello,
One way is to standardize your process and educate users.
You can have the payment runs scheduled on weekly basis. During this time, vendor/customer master data changes shouldn't be done by users. If you are using say MDM portal to control master data, you can lock the changes for certain period.
Also, in a live system, there shouldn't be frequent master data changes to existing vendors/customers.
If it is happening so, you need to look up your master data and do a mass clean up.
Thanks,
V V