[Hofferic]

If you use the "direct open" download mode (the left download menu) the app will look for a copy of the book in the current download directory and, if the file is new enough to be up to date with the last changes for the book in the library, open it without a new download. In all other cases the book will be downloaded again but overwrite any previous file for this book.
So you may redownload the same book but there will always only be one copy (unless you changed its title or author).

I may change the "download for later" mode (the right download menu) to also check for the file date if you would like it to do that, for now it does not to allow for easy redownloading if the file changed but the metadata didn't without manually deleting the file first.