The following is based on MY understanding of it all, and I recommend that you do additional research into the process, and of the consequences and benefits of the different ways to do things. I CERTAINLY would recommend a full backup of your projects folder and all audio (if not per-project already), PRIOR to moving things to the new drive, particularly if only bringing over referenced audio clips.
The Save As dialog box process will copy all referenced audio clips in a project, IF you have the check box called 'Copy All Audio With Project' checked, so if you open a given project on the C: drive, and then use Save As to move it to your E: drive (or whatever it is called), AND you have 'Copy all audio with project' checked, Sonar will only take the clips that are actually used in the project and move them to the new location on E:
If the check box is not checked, no audio will be copied for the project, during Save As. It will leave the audio in the original folder.
I myself would never choose to create a saved copy of a project where all needed audio clips were not present in that project's audio sub-folder. I think it would be too easy to end up with missing audio doing it that way.
Anytime I save off a project, I copy both the project file and the audio sub-folder to a new folder I create for holding the saved version. That way, everything it needs is present.
Keep in mind that if you have audio clips in a given audio folder for a project that you want to keep - but where those particular clips are not referenced, then instead of using Save As to move that project to the new hard drive, I would suggest copying the whole project folder, bringing all audio clips along as an included sub-folder in the copy.
It really comes down to a project by project basis, in terms of what audio you want to keep, whether or not you set up archive folders to have needed audio present in their own audio folders, and what audio you want Sonar to ignore (where it is not referenced but still present in the project audio folder).
You can:
1. Copy a whole project folder to the new drive, to preserve all audio clips, which would include both referenced and non-referenced clips.
2. Save As WITH the 'Copy All Audio With Project' checked, which will copy only audio clips that are actually referenced by the project, cleaning out old/unused clips in the process. When I do this, which is my traditional method of doing things, during the Save As dialog box processing, I create a new folder in the new location to house the saved version of the project, and also create a sub-folder called Audio within that new project folder. Please note that I manually change the project file to match the name of the new project folder, such as from the original Bob's Big Song, to the new Bob's Big Song BK, or whatever, so that I ALWAYS have the project folder and the project file within it matching in name.
3. Save As WITHOUT the 'Copy All Audio With Project' checked, which I think would be a bad option, as it would try to reference the audio clips from their original location.
4. Copy/Paste manually, the contents of a project folder (project file and the audio folder), to a new location - first creating a new project folder (with a new name - such as adding BK to the end of the name), and when I do that I also rename the project file in the new folder to match the name of the new folder.
There well may be additional options for you to consider, and I hope others weigh in on this thread with advice and concerns. :)
Bob Bone