I have to admit I kind of dropped this on the floor after my initial flurry. Thanks for the additional work, pdurrant.
One of the things that has always been a little irritating about Mobipocket (compared with ePub) is that it hard-codes file offsets in links, making it problematic to fix errors in an eBook if you don't have good tools. It's clearly seen as a display format (like PostScript) rather than a source format.
Thankfully, ePub is a lot more sane.