Comment 1 for bug 1407860

If you want to import a file into the book and and entry for the file
already exists in the manifest, you have two possible approaches:

1) Open the opf file and manually remove the entry in the meanifest
2) Run the check book tool, it will show you an error that says some
thing like "Item in manifest is missing" along with an action to
auto-remove the manifest entry. Click that action and the manifest entry
will be removed for you.

After doing either of those you will be able to import the file again.

Someday, if I have some spare time, I may look into detecting this error
specifically and adding an easy workaround in the import file process
itself.

 status invalid