This PR fixes the issue (you can flash the firmware when the serial monitor/plotter is open), but a little problem remains: when you flash the firmware to a board, the sketch on the board is replaced with the code necessary to do the update, so re-opening the serial port is pretty much pointless. I wonder if this impacts the experience
cc: @per1234 @ubidefeo

re-opening the serial port is pretty much pointless. I wonder if this impacts the experience

I don't think so. The reason is that if I am working with the Serial Monitor before doing a firmware update, I am likely to want to go back to working with Serial Monitor again after. So it is convenient for Serial Monitor to remain open, even though there will be no output until I have uploaded my sketch again.

The firmware updater already displays a warning about the sketch being overwritten, so the user shouldn't be surprised to find that no output is arriving in the Serial Monitor. However, they would find it confusing to see the "Not connected" banner persist in Serial Monitor after finishing a firmware update, since that could give the impression that something is wrong.