Conversion from MOBI to ePub and preserving footnote links

[bloodfyr]

I see a lot of posts about converting the other way around and maintaining foot/endnotes, but I can't seem to find a post about going from Mobi to ePub and preserving footnotes and endnotes.

How would I go about doing this? When I do it, they just show up as non hyper-linked numbers in the body of the text. I have a rooted Classic Nook, so I can't install the Kindle app (as far as I know). I'm also a calibre novice, so I apologize if the answer is right in front of me and I'm stupid for not noticing. :<

EDIT - Oh never mind. It would seem that the original MOBI file (as downloaded from Amazon and before I run it through a de-DRM and conversion in calibre) doesn't even have linked footnotes, but they're linked in the cloud viewer.