What seems most likely to me is that the indices are generated
correctly, but texi2pdf refuses to generate the sorted versions.
If I call texi2pdf --debug I do not see any invocations of
'texindex'. May it be that texi2pdf does not call texindex but use
an inlined sorting mechanism that cannot cope with @index, only
\index? I can try if updating texi2pdf cures the problem.
Please try the attached patch and check whether the index reappears.
Note that the entries in the concept index most probably are not
correct (i.e., we want to have both `foo` and `\foo`, which are
different things); I believe I have to play around to get the
functionality back that my hack enabled.