You can do it by following this procedure:
(unfortunately it has apparently been removed from the current documentation, so only available from this 2021 archive of the docs)
To reprogram the D11, simply power it while shorting SWDIO to GND pins.
The board will appear as "MuxTo bootloader" and can be reprogammed using bossac or the IDE Upload button if you selected "Arduino MuxTO" target.
I believe this part is incorrect or outdated:
The board will appear as "MuxTo bootloader"
The board name is actually "Arduino MuxTO", not "MuxTo bootloader":
so, if the platform is installed, Arduino IDE will identify the port the board produces by that name.
From this:
We can see that it uses the MattairTech_Arduino:bossac "tool":
(the 4kb value of the bootloader custom board option menu is specified here)
The upload.native_usb property referenced in the command template is defined here:
Of course ideally we wouldn't need to think about any of that as we could simply click the "Upload" button in Arduino IDE and it would take care of generating and invoking the appropriate upload command for us. But, as @cattledog mentioned already, unfortunately the Arduino IDE support for Nano Every's "MuxTO" chip is no longer so accessible due to the loss of availability of the tool dependency files of the "MattairTech SAM D|L|C core for Arduino" platform.