I'm still a little confused. Here's my current understanding of the situation: The channels that you assign to the insts. on your multitimbral synths do matter as they are linked to your tracks, right? So, you output your flute track to the channel on your synth that is your flute. I always put that on channel. I put oboes on 2, and so on. Each inst. track is output-ed to one of the 16 slots in my synth, corresponding to the insts. I have loaded. The result is all my insts. play the tracks/notes assigned to them. I can also play each inst with my midi keyboard, and record midi as well. So, the channels we are talking about here do matter, right?
The channels that I don't think matter are the ones listed in the Event List (EL). Each note and CC event in the EL will have a channel number. In Sonar, those numbers always stay the same for a given inst, regardless of what you do. You can copy from one inst to another, drag notes from one to another, and in Sonar, the channels "don't follow." The channels will change to the new inst's channel assignment. So, I move a flute part to the oboes, the channels in the oboe's EL will be 2, not 1 (the channel for the flutes - keeping with the example above.).
In Reaper however, things are different. When you move notes from one inst to another, the channels do follow, so the flute part I move to the oboe will still have channel 1 in the EL. Making me think that I need to change them, as those notes now are on the oboe. But if I'm understanding Bruce correctly, no, it's a waste of time, they don't matter, they are overridden by the routing assignments.
Is this what you're saying, Bruce?