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When I upgrade Drupal, even the minor versions, the .htaccess file gets scrapped and a new one is created...
have you ever heard of this type of issue?
This is normal. There has been some discussion of it in connection with drush and there is a sandbox module to generate a .htaccess from the gui.
One workaround is to put your redirects etc in your Apache or Varnish or whatever server config file. Other than that you just have to remember to back up your .htaccess and put it back after updates.
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