Deleting unused files

I'm pretty sure if you delete them from the project then "Save as" to a different folder, your takes won't be carried over. I say "pretty sure" because Sonar does take the non-destructive thing seriously, so if you have a clip that's not trimmed and there's more to the file than just the clip, it will be saved.
 
If you really want to get rid of everything you're not using. do "Save As" and check "Create one file per clip." This creates new files only for the clips that are actually used in your project. You can then delete the old project folder with the 45 million takes.

Well, when I do a simple Save As, and save the project file in a new folder, the Save As Dialog Box has a check box to 'Copy All Audio With Project'.
 
I just tested this to make sure I was correct in my recollections, and sure enough, it only copies over the audio clips that are actually referenced in the project.
 
Prior to the Save As, the original audio folder had 7 audio clips in it.  After the Save As, in the audio folder in the new project folder, there are only 4 audio clips.
 
Bob Bone

You can always Apply Trimming to all clips to make sure you save only what is shown and then do a Save As. This will just save what you want and delete what you do not want.
 
This is the most common and safest way to do it. also make sure you back up all projects so you have at least 3 copies  of each project, all on separate hard drives.. Keep one off site, in case of fire or theft.
CJ