OK, thanks to Kovid's help above, I was able to figure out why converting a book from OEB to Mobipocket strips out all of the <reference> links in the <guide> section of the OPF file except one Table of Contents link and a cover link. It turns out the OEB input contains a module named guide.py, in the directory:
src/calibre/ebooks/oeb/transform
which actually has the
specific function of stripping everything but one cover and one TOC link out of the <guide> section of the input OPF file. Commenting out the last three lines of the
guide.py file (and of course setting the CALIBRE_DEVELOP_FROM variable to the c:\calibre\src directory, if that's where the calibre source is) fixes the problem:
Code:
#if x.lower() not in ('cover', 'titlepage', 'masthead', 'toc',
# 'title-page', 'copyright-page', 'start'):
#self.oeb.guide.remove(x)
I presume this must have some use -- apparently it was designed to choose which cover image to use, if there are multiple cover images specified? But it's having unintended consequences with Mobipocket output...