One instance of Sonar Craig - two projects open containing audio and midi tracks only (no soft synths), I play one project and stop it, then switch to the other project and play it.
I also have two projects open when programming lights - one contains only pre programmed chase paterns as midi clips. The noise happens upon starting playback after switching projects just to copy a clip accross as well. It seems that simply making another project active without even starting playback, then switching back to the original project and playing it is enough to trigger the behaviour.
Yes slarta - you can certainly have multiple projects open and switch between them. I have done this for many years. If by 'on the fly' you mean whilst the project is actually playing, you probably could expect some issues.