"Directory not empty" sudo rm -r -i "file name" not working

First, I would be sure no files are locked

sudo chflags -R nouchg Local\ Storage

Then, assuming you are sure about using sudo and rm -rf on your backup drive, you could tell rm to force things.

sudo rm -rf -i Local\ Storage

This is caused by corrupted entries in the drive. The steps below solved my problem.

  1. Open Disk Utility
  2. Choose the partition/drive
  3. Under the First Aid tab click Repair Disk

The file should be gone after this, if not just try empty trash again. It should work.