I think that the
CWAF_Tool (Cakewalk Audio Finder Tool) works great for this even if you save different versions of the project (like I do). It is also very easy to use:
1- Save any projects you are currently working on. Just have Sonar open and select the CAWF Tool from the Tools menu.
2- Click "OK" on the warning message that appears. Then configure the CWAF as needed by selecting the File Extensions (CWP for project files) and Drives that you want to search. Click "OK" when you're done.
3- Next, hit the "Find" button and wait until it shows you the Status of the .wav files on the bottom half of the window (Referenced, Orphan, or Missing).
4- Click on "Status" to group similar files together. This will make it easy to select a bunch of Orphaned files in one go by draging with the mouse while holding the Ctrl key (alternatively, select the first orphaned file, scroll down and click on the last orphaned file while holding down the SHIFT key).
5- Once all orphaned files are selected (make sure you've only selected orphaned files by looking at the bold writting found at the bottom right corner of the window), click the "Move Wave" button. "Move to" should already be set to "Recycle Bin" so just click "OK". Confirm the file delete by clicking "OK" once more.
6- Another window will appear asking you to re-search drives, so go ahead and do that to make sure there are no missing files.
Don't worry about deleting these files since they will remain inside the Recycle Bin until you permanently delete them, so you can go back and restore them if needed. In case the CWAF Tool finds any missing files after re-scanning, make a note of the project files they belong to and open them. You will see a message telling you that some files that belong to the project are missing and you'll be given different search options. Before you continue, select the option to reference files from their present location, then go to the Audio folder and search for the file it's asking you. Once you select this file all other missing files from this project should automatically be found (but sometimes you have to find a couple of them). Repeat as needed.
If no missing files were found then you're good to go. The CWAF Tool might seem hard to use but it's actually really easy and a blessing if you know how to use it. For more info, read the manual or hit F1 while having the CWAF Tool open.
HTH