Usually what I do is a "Save As " after doing a bunch of edits and deleting old audio tracks & performances that are no longer needed in my project....
When I go to do a save as the dialog box will reference the original project in the per project folder ...
I make sure that I have the copy all audio box on the lower left checked .
Instead of typing in a new name I will just click on the SONAR file itself in the folder and choose that as what I'm looking to keep .
Then I hit save , (usually as normal ) what happens next is the box will come up with the SONAR project information .
After clicking OK a new dialog box will come up stating "the name of the song and this file already exists "
replace it ? that box will have a yes or a no in it ...after hitting yes I'm good to go ...
IIRC , the project has been cleansed of all the extra files I no longer need . Only what I have kept and saved during the save as will now be in my SONAR project ...
hope that helps ,
Kenny