1. Create a new directory for your project. So say your project is named "MyProject", create a new directory on the same level called "MyProject1".
2. Click File / Save As
and navigate to the new directory.
3. Click the "Copy all audio with project" checkbox
4. Save. Your new directory now only contains the audio your project really uses.
You now may either delete the old directory and rename the new one back to the old one (close Sonar first) or just continue with the new one and keep the old one as a backup.