On Fri, May 18, 2012 at 6:38 PM, Anthony tony@tony-mac.com wrote:
answer from Bluehost: "Simple Scripts could overwrite your .htaccess during an upgrade, however Simplescripts doesn't modify any files in an upgrade unless Drupal has outlined that the files should be changed, so any files other than the .htaccess that were modified would be a result of Drupal specifying that they should be."
Which points out that you need to keep a copy of any file delivered by core that you have changed outside of the directory containing Drupal. This includes but is not limited to .htaccess and the sites directory. If you made changes to any file, you will loose it when you let simplescripts do the update. I can only assume that they were at least smart enough to copy the contents of the sites directory for the update or you would have seen other heartaches.