You have MIDI tracks recorded into Reaper or into the VST? If the MIDI is items on a Reaper track, just remove the VST from the track, items won't be touched. It sounds like you are removing the whole track. But if the MIDI is internally recorded to the VST, then you must record the MIDI output onto the track before removing the VST. (right click the arm button for these options)
But what do you mean you are opening Sonar projects? In Reaper?
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