Desperate times call for desperate measures
First I would check that the file is on the Kobo using OS (Windows my computer etc.)and that it is the correct format(epub?)
Then exit calibre and see if it is still there (before disconnecting Kobo)
Not sure what to do next but might help to know when it is disappearing>
Optionally you could add the book using the Kobo software and see if that works.
Helen