I can't believe this hasn't ever come up in the almost 20 years (off and on) that I've used Cakewalk products, but here it is. So I have a large project file with recordings of 6 songs that my band did. I need to basically chop up sections and make a medley for a promo video. I'm not worried about that actual process. I want to basically work on a copy of the file to allow me to later finish mixing the songs in their entirety. I did a "save as" of my .cwp file, but into the same directory (without redirecting the audio portion). If I start chopping up the individual tracks and deleting the data I don't need, will that do anything to the underlying audio files? Or will they remain there untouched? It's about 12GB of audio across the entire project and I would rather not duplicate it if I don't have to (but will if I need to).
 
 

No matter what you do, you should always have a 2nd or 3rd back up copy of the original project stored on a different drive. 
 
And it's as easy as perform the "save as" and re dirrect the file to a new location and make sure you check "copy all audio with project" 
Grab a USB stick for $4 if you don't have a second drive handy. 
 
You can aslo just drag and drop your Project folder to a new location, that's what I do. I then add the date to the folder so I'll know which version it is later on. 

jeebustrain
...I want to basically work on a copy of the file to allow me to later finish mixing the songs in their entirety. I did a "save as" of my .cwp file, but into the same directory (without redirecting the audio portion). If I start chopping up the individual tracks and deleting the data I don't need, will that do anything to the underlying audio files?

 
I've done this lots of times. The WAV files in the Audio folder will not get deleted or modified by anything you do when working within the CWP project and your original project will not be affected.