I've used the 'clean audio folder' utility for years without any problems.
Here's a tip that always works on my system; if you have several hardrives it will take a while to search through them but after that it will take considerably less time to search through the next opened project (unless you re-boot of course)
I always back up finished projects to several backup drives plus also to better quality dvd+r's.
Remember hardives can fail & should be run every so often. I spin them up at least once a year.