Difference in ebook file between Calibre and Nook

I have been using Calibre and my Nook for almost twelve months now with very few problems. But now I have an issue where I have a file that I can look at on Calibre on my laptop and it has 800+ pages and is 1.5MB in size. I have sent it to my device and it appears to be the same size but only has 400+ pages. Half the prologue is missing and it ends part way through the book. I have tried removing it and replacing it - same result. I have sent it to my storage device on the Nook - same result.

Can someone help get me out of this situation?

Cheers
Allyson