File Management...

The cwp file contains relative pointers to the associated audio files that it uses. Basically, they tell SONAR "expect to find that audio file in the subfolder "Audio" [where per project audio] is used" and the like. If SONAR doesn't find them, you need to search for them manually when you open a cwp file in SONAR (SONAR prompts you when loading).
 
That said... if you have used per project audio (highly recommended), you can simply make another "Cakewalk Projects" folder on your archive drive, and move the project folders to them. They will load without issues from that. Moving just a cwp will get you into the finding the audio files loop.
 
The simplest solution, especially if you have a global audio folder in use now, is to copy the ENTIRE Cakewalk Projects folder to the archive drive, then you can delete/clean up the active folder you are using now (you will not lose anything, since the archive is 100% in tact). As you move forward, if you find an older project which does not use per project audio, open it from the archive, then do a "Save As," create a folder with the same name, and be sure "Copy all audio with project" is checked on the Save As dialog. This will create an "in tact" project folder that only has the audio needed to run the cwp inside it. I would also highly recommend only doing this on projects you actually open and work on, since if done as a "computer maintenance activity" it will just get burdensome and waste your time. With a 100% in tact Cakewalk Projects archive, you can always go back to find things if/when you need them.
 
That same archive is something to keep a third copy of, just in case, on an external drive, since Murphy tends to strike at the most inopportune moments in life.

I'm assuming "per project" audio will mean saving projects as "cakewalk bundles"
No its NOT a .bun file.
It just puts all the audio for the project in the Audio folder, and that resides in the Project folder.
<folder>My song
contains My Song.cwp
and the <folder>Audio
that contains all the wav files for the project.
Now if I want to copy/move the project I can "pickup" the folder and "drop" it anywhere I like.
ie. Thumb drive to take it to another machine, an internal backup drive, or my external backup drive.
 
I would suggest opening each project and do a "save as" and tick the box that creates the Audio folder,
then tick the box that copies all audio to that audio folder.
Storing all the audio in one "Master" Audio folder (one that includes all the wave files for every cwp);
is a recipe for disaster, at least in my opinion/experience.
 
As to your midi question:
I leave all midi in a track folder named MIDI and then I archive that folder after freezing all midi tracks.
Just the midi is there, the frozen tracks are now wav files and have there own track for mixing.
If I want to revisit the drums, keys or bass; I can unfreeze and edit those tracks.
 
HTH,
T

Well start with all new projects and any you are currently working on.
Then open 1 or 2 every session and do your "save as"; eventually you'll get it all done.
I try to eat the "elephant" one small bite at a time.
T