@Michael McNamara I'm pretty sure you could. What service would the EDI hit inside NetSuite. I am assuming it would RESTful API or Web Services. Either way you can trigger user event scripts with that context
I am wondering could you just do a search to group by that vendor and not even worry about checking a checkbox? Or if you need that checkbox checked, could you just have the vendor pass that directly through the EDI (assuming it can map to custom fields in your instance)