It should work, but it could be a timing issue. Does the batch file contain the right content in your full routine?
Instead of using the "auto open" on the export, add another script step: Send Event, with the option to open a document, and point it to where the batch file. That should give FM a little more time.
Do you use 'GWSend calculation field' as global ?
If not, found set is different after import.
How do you 'generated invoices' ?