How did you try to delete the file from within linux? IIRC you are using ubuntu--correct? Did you use the nautilus file manager? That creates a .trash folder so it could be trying to move the file from one part of the internal memory to another and generally getting itself in a real tizzy.
Your iliad will be mounted in /media so you could try opening a terminal and
and figure out which one is your iliad (I think it will be the user name you use for the iliad), then cd to the books directory and delete the file using rm. Also try to find .trash and remove that.