I think that opening the file as you are should be OK, since the file is not being truncated, the data will most likely be written over the existing data.
As I said, the OS can move files around in the background, for example when you edit your infamous book, the word processor probably writes the new version to a new file, and then deletes the old file and renames the new one to the correct name. This means you now have two copies of of the file on disk, one in the actual file, and one in the deleted area of the disk. This may happen lots of times, unless you write the whole book in one sitting, which would probably be an adventure in itself.
I think finding all these areas and removing them would be very tricky and would require intimate knowledge of the OS involved.
A defrag after the delete would probably make anything much harder to recover, and you can probably say you were just doing it for performance reasons
