I managed to get the machine to talk to the network again by issuing a static IP to it from my firewall and matching that IP in the controller.
Now that its communicating over ethernet, the overwrite error no longer occurs. So it seems that particular issue is usb related.
Can you please mark this one as resolved.
I guess the underlying cause of what happened was down to old firmware on the machine conflicting with something in LB2.1.01.
Since updating to LB 2.1.02 and updating the firmware, connecting the machine via Network rather than USB. It has since operated flawlessly.
Hopefully someone else out there in the world finds this thread useful in the future should the encounter the same problem.
Thank you to everyone for the help to get it sorted also. Very much appreciate all taking their time to lend suggestions and ideas.