For anyone else experiencing a similar issue where your EMX or Cobra seems to loose it’s ability to remember EWRs try the following:
Uninstal and reinstall the latest GHI SDK.
Access the EMX/Cobra through TeraTerm via the Serial COM port - it can be confusing to work out which com port the USB connection refers to, but it is possible (mine was 7)
When connected type E then Y - only capital letters work by the way - this erases all the memory.
Then type X to get the board ready to recieve the new TinyBooter file. You will see CCCCCCCC… appear in the TeraTerm window when it’s ready to transfer the file.
In the menu select: File > Transfer > XMODEM > Send …
Navigate to the TinyBooter firmware in Program Files > GHI Electronics > EMX > Firmware > TinyBooter and send that .GHI file.
Then you need to run MFDeploy and update the firmware with the HEX files found in the above ‘Firmware’ directory.
Thanks to GHI chaps for this solution.