Remora on NVEM board - unable to upload new configs

I managed to get Remora uploaded to an NVEM v5 board, thanks to Scott's detailed video instructions. The board has the RT1052 chip and I was able to make a donor STLink into a DAPLink and upload the firmware by compiling the latest Remora-RT1052-cpp source. I could see it working by toggling the eStop in software and seeing the LED light up on the board so I know it was responding to LinuxCNC. Just like in the video. 

I then successfully uploaded the full_config.txt with the upload_config.py script, I managed to get past needing to install the TFTP package via PIP successfully. I did manage to get the config file (the supplied unmodified config) uploaded to the board the first time but now I'm trying to make updates to the config and it no longer uploads. The script confirms it's valid config, but now I get a time-out error. I can still ping the device and get responses, something else is blocking it. 

I've already de-soldered the pin headers - and packed away all of my soldering gear. I could re-solder it and re-flash with a fresh firmware, but ideally would like to avoid that in case this happens again.

Seems the board is now bricked and won't accept new configs. The LED eStop indicator on the PCB is lit permanently and I can no longer toggle it in software.

Any ideas how I can get this up and running again? I've tried to be as specific as possible. I'd love to share some screengrabs and stuff, but the system is set up offline in another room. Let me know what I can provide to troubleshoot? I can get the computer connected to the internet to share configs and logs and other bits and pieces if that helps. Just thought maybe someone knows an obvious answer?  

forum.linuxcnc.org/18-computer/44828-rem...cnc-board?start=2080

take it to here,

but if flashing the config worked before and now it wont work, you will probably need to do a full chip erase to overwrite the sector, then reload the firmware and config.