I'm facing same problem with my Yun board running "OpenWrt-Yun built on Nov 14, 2014" with "sd expansion" as described on https://www.arduino.cc/en/Tutorial/ExpandingYunDiskSpace
The Arduino side has standard bridge sketch loaded from example folder.
If I give only "reboot" command on Linux side via ssh, Linux hangs and is no more reachable via ssh.
Same behaviour If I give a combined "reset-mcu" and "reboot" as described previously.
Linux side restarts correctly and reachable via ssh only if i insert a delay of some seconds (4) before Bridge.begin() in the setup section on sketch on arduino side, and of course using combined reset-mcu reboot.