My preferred way of doing this is to Save As the project to another folder, being sure to select Copy All Audio With Project. Then, the audio file in the new folder will contain only files the project is actually using.
Delete the original folder, and copy the Save As folder back to the original location. Done.
Sometime this can free up surprising amounts of storage space.
As I've mentioned a few times on here, I once deleted all my audio files, for all my projects, using Clean Audio Files. I'm sure it was my fault, but it happened, and I don't want it to happen again.