When I'm finished with a Melodyne track I clone it then make it into a normal track, so I have a track that's away from Melodyne. I then archive off the melodyne track (and hide it). That way you are covered.

CakeAlexS
 
When I'm finished with a Melodyne track I clone it then make it into a normal track, so I have a track that's away from Melodyne. I then archive off the melodyne track (and hide it). That way you are covered.

Yep that would solve the problem, if all the ARA stuff got put somewhere else.

I save a backup copy of the project at the end of every editing session. I only backup the main CWP file, which is always under 2MB in size. I don't normally bother copying the audio files, since I don't edit them so they don't change. This works well for me. I have very rarely needed to retrieve an old audio file and whenever I want to want to open an old version of a project, the associated audio files are usually still intact anyway.
 
A full backup makes sense for a just-started or just-completed project though.

I all so backup  as OMF Files

Kev999- I don't normally bother copying the audio files, 
 
 There are many way's we can use Sonar. All of use have our sliding scale ratio of MIDI /AUDIO involved in any given project. 
The above would apply to say, electronic music, where there is 80%-100% MIDI. 
But for people who record real bands/ instruments we are talking 80%-100% audio tracks. So saving only the CWP file would result in opening a very blank looking track view. 
 
I have always kept everything to do with any given song in it's own folder. Lyrics, scratch, live recordings, track sheets, midi files, CWP and most important the Audio folder. 
So easy to drag and drop this container to another drive.  
I keep a external drive backed up regularly,  and use these files sometimes when I'm away from home. I use a master folder and dating system to keep track. 
 
I also perform a "save as" to my 3rd DATA drive after spending any time working on a project. At any point I feel like I'd rather not take a chance on loosing work. Good Habit for everyone!  
In the 8 years using Cakewalk and Cubase, I have never lost anything I recorded. Only changing the clock rate has caused me an issue with opening files. 

Kev999
I save a backup copy of the project at the end of every editing session. I only backup the main CWP file, which is always under 2MB in size. I don't normally bother copying the audio files, since I don't edit them so they don't change. This works well for me. I have very rarely needed to retrieve an old audio file and whenever I want to want to open an old version of a project, the associated audio files are usually still intact anyway.
 
A full backup makes sense for a just-started or just-completed project though.

What would you do if you had to recover audio clips from some client or musician that was not readily available and/or inclined to record their clips over again?
 
The scenario would be a hard drive failure during a project.  Maybe I didn't read your post correctly, but it seems like you are exposed to that situation, albeit a generally small risk.
 
A curious Bob Bone
 

I didn't say I never back up audio files. It's just that I don't keep making lots of backup copies of the entire project which would result in lots of duplicate audio files and fill up hard drives very quickly. On the other hand I routinely save CWP files without worrying about disk space.
 
 

I'm firmly in the camp of backing up all of my projects, including all associated audio files.
 
I simply drag & drop my entire Cakewalk Projects folder to an external drive. When it's finished, I rename it and then delete the earliest backup from the backup drive, constantly maintaining at least 4 versions including one called "ARCHIVE - DO NOT DELETE" which contains a lot of earlier projects.
It takes about 30 minutes - just time enough to make a coffee and get the duster/vacuum out

+1 per folder, as Scott said.

Regarding the Melodyne files and where they live....

I was just reviewing through the Melodyne tutorial from Groove3. The Melodyne files get saved in a couple Melodyne specific folders unless you change a setting.

While in Melodyne, under the Settings menu in the top left there's a selection for File Manager. Select that. That brings up a dialog called Project Path for Transfers. in that dialog at the far right at the top there are three dots like browse dots. Use that to browse to your Sonar song/project folder and you can create a Melodyne sub folder in there for this path.

If the question hadn't been asked I might not have noticed that little tidbit.