On Mon, Feb 15, 2016 at 2:56 PM, jonetsu@teksavvy.com <jonetsu@teksavvy.com> wrote:

A few moments ago I stopped jackd, without taking care of stopping
Mixbus 3.1. There were some edits not saved (not much as I save very
often) and Mixbus would not save them when exiting, because jackd was
gone. This is not likely to happen, that jackd goes away, although in
such cases data should be saved nevertheless.

The "data" includes signal routing, information about which is lost once JACK has exited (or just disconnected your client). That is why Ardour and Mixbus refuse to save under those conditions.

Use the ALSA backend and this problem goes away.