I delete a whole directory under the root on an USB key before doing a backup. It's easier to avoid to keep files I've definitively deleted. This directory is very complex and it's difficult to search all the "bad" files.
Example, my key contains several directories : dir1, dir2, dir3. Under dir1, I have other directories dir21, dir22 with files in theses directories. dir21 contains file1, file2...
And I use this key to copy file between 2 computers which are not on the same network. I wanted to copy files from the USB key to the second computer, but I deleted dir1 from the USB key instead of the PC disk.
When I launched Recuva, it didn't find dir1, neither dir21, dir22, neither file1, file2...
It found files which were under dir2, dir3 because these directories were not deleted.