One aspect that complicates things is that there are four different
lilylib files that Python can consider to import:
../usr/share/lilypond/current/python/lilylib.py
../usr/share/lilypond/current/python/lilylib.pyc
../usr/bin/lilylib.py
../usr/bin/lilylib.pyc
When experimenting with the 2.8.5-1 package, it seems that convert-ly
(and the other Python scripts) work well as long as at least one of these
four files is present.
With the 2.9.13 package, there is some problem with
../usr/share/lilypond/current/python/lilylib.py
just as you say, but as soon all the other three files seem to work well,
so if you just remove it from the distribution, I guess everything should
work well. Same goes for convertrules, where everything works well
as soon as you remove the convertrules.py file in .../python/.
Unfortunately I don't have the Windows competence to discover what
the problem is with these files.