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Trouble upgrading to QGC 4.0.2

When I try to upgrade from 3.5.4 I can see these commands and then nothing happens:

Attempting upload from file /home/pi/companion/fw/ardusub.apj
Stopping mavproxy
Flashing Pixhawk…
Loaded firmware for 9,0, size: 994240 bytes, waiting for the bootloader…
attempting reboot on /dev/autopilot…

The same thing happens when I try to restore the factory default firmware.

Any advice would be appreciated.