Renamed update hook causes preventing updating site on Aegir based systesm

We are trying to update a site having this module from 1.0 to 1.1. The site is hosted on a Aegir based system.
Now Aegir does not allow to update site because there occurred renaming of update hook course_relationships_update_6402() to course_relationships_update_6400() (in commit 7d4f35406f619d9af2be011397b72097a4aa4f79 with comment "Fixed various issues with aggregated credit.").

First of all, do we really need update hooks course_relationships_update_6401() and course_relationships_update_6400()? Its numbering indicates they are for Drupal 6. For Drupal 7, they are supposed to be in format 7XXX.

Also, renaming update hook is not good idea. It will break systems.