"With regards to your question about wonder why I'm saving files as .mid, why wouldn't I? I am using the files to drive a sound module for live stage performance." It helps us understand what your trying to do. I now have a very clear idea of what your doing.
I used to use midi files back in the 80's for my backing tracks so been there done that.
And I'm totally aware of the need to kill certain tracks if say that night you have a real bass player.
Back then a friend of mine used a Roland Sound brush and a Dr Synth sound module which all you had to do was push a button to toggle playback channels. The instrument sounds were pretty good in those days but now would be considered cheesy.
I still have my Korg 05 R/W module which was my band in 1991, I got tired of lugging around an Atari computer and in mid 90's switched to Sony Mini disks for a decade. I recorded all my sequences to mini disk using the Korg as a sound source. The transfers had to be in real time at first, later Sony came out with software for drag and drop.
This was cool, was the exact same sound live in a very small box. But I had to pack around a bunch of disks and set lists where not flexible.
But My son started playing bass so now I needed tracks that were just the drums and keyboards. PITA. it was easier just to drag the old Atari around and mute the bass channel in the Korg.
I got my first Laptop in 2004 and have been living in playback heaven ever since.
With the much better VST synths that have hugely improved since those days I still use my old sequences and breath new life into them with Sonars amazing pallet of sounds. My Korg has some pretty cool polysynths but the drums and bass are terrible, I can't believe I subjected all those people to that for almost 15 years!
I've been using WAVE files played back in Win Amp since 2004. At first I used close to the same format as the Korg because all I had was TTS-1 in Guitar Studio. I started recording real bass too. The drums are what have been improving over time for me as I progressed through Session drummer, AD2 and now I'm loving Strike2.
I have no need to change my playback live, it's exactly what I want night after night.
My new project is to use Home Studio instead of Win Amp and have multi channel output and midi back to change my Effects for each song, just like I did in the 80's. Have you ever though about using Sonars playlist? or is this why your wanting muted channels?