I've spent the last couple of hours unsuccessfully trying to hunt down
the update-info-dir script that recreates the "dir" file from scratch.I don't know about update-info-dir, but there is fix-info-dir and gen-dir-node in the util/ subdir of the sources, and you can get them from browsing the CVS repository at http://savannah.gnu.org/projects/texinfo/ if you don't have the sources already. I've never run them myself and can't say for sure that they are what you want.
