I'm familiar with using USB mice and keyboards, because Windows CE recognizes them as "Human Interface Devices" (HID) and there are fairly generic USB drivers for them.
The idea I'm familiar with for barcode readers is that they behave like a keyboard, so when there's a read of a barcode that represents "1234ABC", the barcode reader behaves like a keyboard and sends "1235ABC" to whatever field has focus on the PanelView. Generally the barcode reader also includes a carriage return byte so that the scan behaves like a text entry followed by the enter key.
I have never seen this implemented with a "serial" barcode reader. I would imagine that requires the Kepserver UCON driver. Using the UCON driver for string input is one of the simplest things you can do with UCON, but in my experience everything with that driver is tricky.
So my stack of questions is:
1. What firmware revision is actually running on the PanelView 600 ?
2. Are you using the UCON driver or using a barcode reader like a keyboard ?
3. If you are using the UCON driver, what revision are you developing in on your FactoryTalk View Studio PC ?
4. What is the name or number of the RA technote you are following ?
5. Have you tested the application on your development PC ?
I realize it must be plain as day to you, but why do you think you have to re-load the application instead of just cycling power ? When you do cycle power, is the *.MER file still present on the terminal ?