Please dont keep trying to upload firmware, especially as the VEMS is functioning correctly.
The firmware does not go 'off' its stored in the Microcontroller's Flash memory it can only be effected by direct Flash programming.
It seems like you have a comms issue, are you using a USB to serial adaptor? Could you have a program that is trying to use the adaptor too?
If you get a comms issue while you are uploading then you will have a system that is dead in the water with no way of rescuing it.