When session tdsls4404m000 is executed and there is an EDI invoice in the batch of invoices, a message box is displayed stating that an EDI message is being generated. The user must press the OK for the program to continue.

Right now, we have a job scheduled to print invoices and I think this message box will be a problem. Is there a way to eliminate this message box?

The message is hardcoded so you cannot surpress it.
But it is no problem if you schedule 'Print Invoices' in a job: the message will end up in the 'Job History Messages'.

regards,
Robert