im not sure I understand how that happens.
I use the clean audio folder loyally after every 8-10 projects.
and I've noticed it scans my external drives as well. but it always prompts me with a list of files to be deleted.
Note: Photo is older / Sonar 8.5
Typically after cleaning all my folders (before I archive them) I use the CWAF Tool. This helps me find redundant, useless files or files that no longer go with projects.
I would like to see an update to this tool though, its old and slow as molasses. However once you scan one project using the clean audio folder utility, Sonar remembers these folders so the next project scanned goes a lot faster.