In X3, I was able to start Sonar without my Advance 49 turned on. If I decided to record, I'd turn it on and receive a "do you want to load" message. There is no such message in CB.
 
Additionally, if I open a project without the Advance on, all the midi tracks inputs are lost. When I turn on the midi controller, the tracks do not update themselves and I have to manually reroute all the inputs, and I've seen it where I've had to reroute the audio outputs.
 
Has anyone else come across this or is there something I'm missing?
 
Thanks,
Timbo

It is actually up to the midi driver for that device how smoothly these things work. Example, My Roland controller can be turned on after Sonar is running and I get that "do you wish to connect" message. 
My Akai Keyboard does not and I have to close Sonar and re open every time. Same computer. 
So while using the Akai I always try and make sure it is on before I open Sonar. Simple. 

They have tried to improve MIDI detection in some update (if I remember correctly, during 2017 updates). But they have just made it worse.
 
Even in case it asks, I have not seen Sonar changes input settings in already opened project.
 
I have thought that all is "natural" and comes from drivers. Till I first was surprised other DAW has no problem with that and later by programming MIDI communications myself.

Thanks guys. Funny thing is that it asked in X3 and doesn't anymore.
 
Learning curve!

Sorry to resurrect this, but it happened again and I realized I'd forgotten to tell you that not only are all the midi inputs messed up, but each midi output is moved -1 up the list of midi/audio tracks. So I've got the drums playing the bass and the piano playing the drums etc. Sounds cool, but required 10 minutes of swearing and rerouting ... this never happened in x3.