tdehan
I'm using a SR18 for drums and a Yamaha MU50 Tone Generator for some fill in sounds and effects besides also using for drums as well.  I am running Sonar through my Microsoft Surface Pro 4 connected to those devices.  
 
It certainly would be ideal if I was able to mute certain tracks.

I love threads like this, because I usually end up learning something.  The question of .mid file handling is a good one.  I am working with some .mid files in Sonar now, so any help to better understand how this DAW handles MIDI events is very useful.
 
I'm still puzzled about the muted track thing, though.
 
If using Sonar to drive the sound generators, why not save a copy of the MIDI file as a Sonar project file with the desired tracks muted using the track inspector mute buttons?  Then use the Sonar project for the performance?
 
I can understand why if you are exporting a .mid to a hardware sequencer or workstation, but since you are playing back with Sonar through a Microsoft Surface Pro 4, why be limited to the .mid format?

If the song is 100% midi, you can save and open using a CWP file. The CWP is where Sonar saves midi. And the bonus is then everything else is saved including the muted tracks.
The only reason to use midi files is to open them in another app. If your opening them in Sonar, use CWP. They are almost as small as midi files. 

Yup, I also found out the hard way (don't ask) that if you open a .mid file in Sonar, make some changes and hit save, the file is saved back to the .mid file.  If you exit Sonar after that, then whoops!!!
 
To keep non-MIDI supported settings for the project, you must select "File > Save as > Save as type: Normal" to select the .cwp format that stores all of your additional changes.