Since you tried to run a firmware update while you were having trouble connecting, the first thing that we need to do is figure out what the status of the firmware is.
What I’d like you to try next is manually entering bootloader mode on the EBB:
(1) Disconnect power to the AxiDraw. (Leave it disconnected until communication is re-established. The USB cable can power everything except the motors.)
(2) Disconnect the USB cable. It may be easier to do this at your computer or at the AxiDraw — either way is fine.
(3) Press the pause button on the left side of the machine.
(4) While keeping that button pressed, connect the USB cable.
(5) Release the pause button.
If this works, then the EBB should go into a red-green rhythmic-blinking “heartbeat”. If so, that’s a good sign. While it’s still in that “heartbeat” mode, try to run the firmware updater program.
When the updater program runs, it will try a few different things. It could run into one of several different errors and may report them to you. If it either prints “Firmware updated successfully” or a firmware version string like “EBBv13_and_above EB Firmware Version 2.6.4”, then it likely succeeded, even if there are other error messages.
If it does not succeed — if it does not appear to be able to locate the device whatsoever — then the most likely culprits are the USB cable, the USB port, or the computer needs to be restarted. If you’ve restarted and still see a failure to detect the device, then try a different USB cable if you have one available.
If the firmware update does succeed (or likely succeeded), your next step should then be to try again in Inkscape, and see if it can connect.