have this on one project with a external VST plugin on opening the project.
when I turn the VST off and on again, extreme cracks are gone.
I would not try bouncing to tracks as I'm not sure if it will add 1 roundtrip of latency to the audio files, like you would get on an export.
First thing I'd try is to remove the plugin, then save the project with a new name to a new folder, as a bundle file.
Then open/close Sonar and add the plugin again and see if it's gone.
If not, I can emagine it must be impossible for the music software industry to make all software out there compatible to eachother...