So let's say a "friend" of mine has been a bad boy and recorded a bunch of songs using the past three or four versions of Sonar and not paid any attention to where the project files were saved, resulting in a number of projects that are still playable, but for which the audio data is stored in seemingly random locations across multiple hard drives. Now my "friend" wants to repent and correct the error of his ways. What's the best way to clean up these messy projects? Ideally I want he wants to get them into per-project folders, as I he should have done in the first place.

Make sure the "Use Per-Project Audio Folders" option in Preferences > File > Audio Data is enabled. Then open each project and use the "Save As" function making sure the "Copy all audio with project" option enabled in the "Save As" dialog to recreate projects with per-project audio folders.

Choose Edit > Preferences > File > Audio Data and check "User Per-Project Audio Folders."
 
Then create a folder for each project in the Cakewalk Projects folder, call up the project, and Save As into the appropriate folder. Verify that the Project Path and Audio Path on the bottom of the save dialog box is the folder that was created to hold the project.
 
Make sure "Copy all audio with project" is checked. To save the absolute most space, check "Create one file per clip" but this basically truncates the audio to whatever is on screen - if you want to roll something out further, you won't be able to.

scook types faster than I do.
 

Thanks guys! I'll tell my friend. (He didn't expect it to be that easy...)
EDIT: This will copy, not move, the existing audio data to the new project folder, right?

Advise him to read the documentation on saving, there's lots of useful information in there.

Anderton
Advise him to read the documentation on saving, there's lots of useful information in there.

Craig - He's been reading the docs and saving things correctly for a while now. He just wants to clean up old messes that he made before he was enlightened.

Yes "copy". You'll still have to go on a safari to clean out the drives of all the older files.
 
 

Just don't delete anything until all new versions have been tested and proven to be stable. 
Back up storage is huge and cheap. Before I do anything I would drag and drop the whole folder to a back up drive and name it "Old FKDUP files" or something. I actually never totally erase any copy of any project folders. I just keep my working drives tidy. 
 
Myself I would do as Craig said and make new folders on a data drive for each project. I then open the messy projects and do the SAVE AS and point them there using  the copy all audio etc. 
 
I use a dating system for main "album' folders which will contain the songs. 
 
Example : Sock Monkey Sock Waves album Aug 22 2014. 
That way when I look in a back up drive I know when it was last updated. 
 
 
 

sock monkey
Just don't delete anything until all new versions have been tested and proven to be stable. 
Back up storage is huge and cheap. Before I do anything I would drag and drop the whole folder to a back up drive and name it "Old FKDUP files" or something. I actually never totally erase any copy of any project folders. I just keep my working drives tidy. 

EXCELLENT advice.