When you delete files from a flash drive or external hard drive, files go to a trash bin located physically in the drive.
But in the GUI, both the external drive's trash and the computer's trash are coalesced into one. When you empty the trash you are emptying both trashes. That also seems to be the case for OS X and Windows.
I could, obviously, delete the trash on the flash drive using the terminal, but it seems to me there should be a way of emptying the flash drive trash without emptying the computer's trash using the GUI.
Is there one in Ubuntu ?
When you open flash drive press CTRL+H or through menu View > Show hidden files, hidden folder should appear
.Trash-1000
or similar. Delete this folder like normal file, you will be prompted with ask "Remove it permanently?", press delete button. Or delete this folder by selecting it and pressing Shift+Del.