Well lets take a look at what you actaully did there--
sudo cp -avr /home/chris/.thunderbird/ /media/disk
SUPER-USER-DO COPY --archive --verbose --recursive FROM /home/chris/.thunderbird/ TO /media/disk
So basically you added files to the key but you didn't remove anything or format in any way shape or form.
If you wish to DELETE the contents on the key use REMOVE
sudo rm -rf /media/disk/*
As with anything related to deletion or removal of files I suggest you have a tested good backup on hand... etc.
Generally you're not going to format something unless you need to change the file system that resides on it.