That’s a big project with lots of moving parts. Do able, but not trivial.
First note: Barcodes are nothing more than machine readable text, and just speed up what you would otherwise do with a keyboard. The actual barcode part is trivial.
We use bartender and I really like it. We use the automation license, and I think that’s what gets you what you need for triggering labels with a file drop.
I don’t use any epicor functionality with regard to bartender. They lock you into certain forms and tasks, and there really isn’t good way to change it. For all of my stuff getting sent to bartender I custom code my output. See the thread below to show you how to do that.
For the rest of your project, it’s up to you to come up with the logic for what does what. You’ll probably have to get quite of bit of code to be able to do it, but it’s possible.