Arduino DUE "No device found on COMX" - Flashing?

Official Hardware Mega Due
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I am not sure what's going on. I'm trying to communicate with 4 boards using a USB hub. I have a USB-B cable connect to Hub, and individual connections back to hub from programming ports.

I had been swapping USB cables and testing programming the devices. It's possible that maybe the USB-B cable was bad, because when I attempted to program a device, it compiles but doesn't even begin to download. Instead says "No device found on COMX"

Once I receive this message it is unrecoverable. My computer reconginizes the device as an Arduino Due (Programming Port), but any attempt to download and the RX light flashes twice and then stops with the error message "No device found on COMX".

I was even able to program a NEW device several times on the bench directly connected to my laptop. Then when I connected to the USB hub in the same configuration as others, it became broken in the same manner.

I've tried using reset and erase buttons to no avail. At this point I have thrown the suspect cable in the trash but because I am unsure what is causing the issue I can't rule out anything. I can program 3 of the devices with this specific setup for now, but I'm unsure if it may return unexpectedly. I would feel more comfortable if there were a way to recover the failed devices.

I suspect all of these problems to have arisen from programming, like maybe the act of programming caused the thing to lose its firmware. Is there a way to re-flash these units to get them talking again?

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After playing around with this a bit I see that I am able to load a program through the Native USB Port. It appears as though the programming port is complete toast. Aside from the fact the RX light flashes when receiving data.

Is there any downside to using the Native port as opposed to the programming port?
Any recommendations are appreciated.

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I've been checking some things on the boards. Strangely it doesn't appear that there are any issues with the resistors or fuse on the programming port. I'm unsure how to check the ESD suppressors, but I would assume these to not be 'required' to program.

The ATMEGA16U2 chip is receiving signals because apparently it drives the RX LED and this is working. For some reason, it does not respond to anything (not TX LED). How could a programming port cause the chip to fail? I tried issuing a software reset (RESET_CMD), ERASE_CMD and even tried the RESET PIN24 (low).

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