If the Leonardo responds to the booting information of the Linux; it is very likely (not to say it is guaranteed) that the Linux will not finish its booting process.
Why is this?
Are all the ways to 'reboot' the linux side making use of the 'reboot' command?
E.g. suppose the linux side has completely crashed, and it can not execute anything anymore, how would you be able to recover from such a state.