I've been using Czkawka. Select individual disks (not the pool) in "Folder to Search" and then run "Empty Directories" and delete them all.
My workflow has been:
- Run Drivepool balancing by space used
- Stop Drivepool service
- Run Czkawka Empty Directories
- Run SnapRaid Sync/Touch/Scrub
- Start Drivepool service
It's been working pretty well. You can also create a .bat to make it even easier.