shrike
...midi IN on this track is set to A-PRO MIDI Ch. 2, midi OUT to Independence 1

This is what I'm getting at. You're recording events as channel 1 on track 1, and channel 2 on track 2, but you don't have a forced output channel set. So if you move the MIDI events from track 1 to track 2, they are still going to drive the instrument on channel 1 in the multitimbral synth.
 
You need to set forced output channels on the MIDI tracks corresponding to the channels of the synth. In the Inspector, [C]hannel is the first parameter under the MIDI FX bin. That, or you need to select the copied events and change their channel using the Event Inspector or Process > Find/Change
 
Most users no longer record events using different embedded channels; they just record everything as channel 1 and rely on forced MIDI channels to control routing.
 
 

shrike
...midi clip which I've recorded with IndePro and saved into Projects folder (using drag-drop technique, just drag out of lane and drop into folder) contains information about which midi channel it was recorded on...

Does that mean that your problem clip was not created within Sonar?  When using imported MIDI, it's usually wise to start by opening Event List View and deleting all the unwanted items at the beginning of the clip.

Brundlefly, thank You very much for this suggestion. Unfortunately, I didn't have time to check out Your solution, but I'll do it today, hopefully.