The answer relates to changes to Time Machine backups in Lion.
My understanding is that when a TM back up is attempted when the back up disk is not connected, a back up is made in /Volumes/MobileBackups.
These back ups do not go away the next time TM runs with the back up disk connected. I am not sure if the OS will eventually reclaim this space.
You can disable the local back ups by running one of the following commands (depending on your version of Mac OS):
sudo tmutil disable localsnapshot
# for older versions:
sudo tmutil disablelocal
After you run this command /Volumes/MobileBackups is deleted.
I'm sure there is a good reason for the local backups and I don't necessarily recommend disabling them, but they were - in combination with some large deleted folders - the cause of disk space appearing to be still in use.
You can re-enable mobile backups by running:
In MacOS Ventura or later:
sudo tmutil enable localsnapshot
In previous versions:
sudo tmutil enablelocal
More info at Mac OS X 10.7 Lion: the Ars Technica review