If I was doing this, I would do a Save As PRIOR to deleting data from the mixed version of the project - just seems safer to do all of the deletions and such where there is NO way to potentially have wiped out good data.
I would then select all the tracks and then click on Tracks and then on Wipe Track, which will get rid of any track content present in the selected tracks, but leave the FX bin and track properties for each selected track alone.
Here is the link to the Track Wipe functionality:
http://www.cakewalk.com/Documentation?product=SONAR%20X3&language=3&help=Menus2.106.html If you wanted to create multiple track templates, you could select the tracks to be part of a given template, and export those selected tracks as a track template, repeating for however many track templates you wanted to create out of that project.
I DO have a question, and am not currently in a position to test out something. It is my understanding that Sonar creates some sort of internal connection to audio clips in the project, and the path to those clips. If Save As is used to create a project, and the Copy All Audio option is not checked, and Sonar then would not copy over any audio to the new location, and then the tracks are wiped in the newly-saved project, and Sonar is internally pointing back at the original audio clips, would a cleanup of the audio end up deleting those original audio clips? I would hope the answer to this would be no.
Bob Bone