The following pertains to adding EPUBS to the iOS version of iBooks...

If you are having a "missing resource" error in regards to adding an
EPUB to iBooks, you may need to change the file-name, which is not
the same as the title meta-data. The title meta-data is what is used
when an EPUB is listed on iBooks. PDFs are treated differently.

If simply changing the file-name of the EPUB does not work, you may also
need to change the EPUB's title-related meta-data. You can do this using
the following in a terminal (install 'Calibre' first)...

    ebook-meta -t 'Changed title of book' '/path/to/book.epub'
    
You get a bunch of 'ebook-*' command-line tools when you install the
free and open-source ebook manager 'Calibre'.

I believe that the main reason this type of error happens is because at
some point you had a copy of an EPUB with the same file-name or title 
meta-data but you decided to replace it with a newer or better version. 
Running iCleaner on a jailbroken iOS device will not help.

This is what happens when an operating system has an "everything is a 
database" philosophy rather than "file."