refreshLinks.php has also erased my categories in the past. Though mainly automatically-added categories (i.e., categories that are added to the page by a parser hook function). I never took the time to figure out what happened -- it was a while ago.
DanB
-----Original Message----- There were no error messages during refreshLinks.php, just the progress indicator. Maybe there is something in my LocalSettings.php that is incompatible with the maintenance script. Or some other enviromental issue...