I'm not sure whether there is a way to check which port has the device connected without writing code, since you need an explicit VISA reference to a specific port to use the VISA VIs (at least the ones I know), so you have to know the port. You could write code to cycle through the ports until one is found that doesn't have an error.
I only have experience with one serial to USB converter, and that one, once installed, keeps a specific port (in this case, COM 4) and doesn't change. Even if the device is connected and disconnected on a regular basis, you can force the user to have only one available port in the hardware. Then, you configure the program once and save the data.
It's possible that the second Bytes at port VI runs too soon and so you don't get all the bytes sent, because they didn't get there yet. Did you try doing what I suggested (using a -1 timeout and a VISA read)?
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