The advice I saw a long time ago that I really liked and use is to save the project to a new Project folder and let it carry over all the audio files that are still in the project. Then, when you feel safe doing so, you can delete the old project folder(s). I did this on my last project and it went very well. After picking and comping the good takes and bouncing etc. I saved the project once in the existing folder then did Save As, changed the Project Folder name (Sonar automatically changed the Audio file name) and resaved. I could see all the audio files being rewritten. So a project would go from several GB to under a GB.
I'm paranoid, so I only deleted the old folders after they were a few rounds old.
I hope that helps (and wish I could remember who recommended it to give them proper credit).