Ugh you hit something I've been trying to figure out. I buy a omnibus in epub and convert it to mobi in Calibre but I lose the Navigation because the spine and ncx file don't line up!
The thing is I don't know how to fix this most of the time because epub's ncx file uses a text entry at the top Level and it's not link to any file.
If I leave it in the NCX file it doesn't translate well over to mobi and I loose the ability to jump chapters. There's probably a simple fix but I've yet to find it.