I ran into this issue twice upon upgrading wordpress using the automatic update wizard. The upgrade automatically expands wordpress including the .htaccess file. I happen to make some changes and tweaks to the .htaccess file which get overwritten with the new version after upgrade.
Yes, I can (and do) make backups of the .htaccess file now. But it would be good/nice if the automatic upgrade wizard could somehow merge the contents of the out-of-the-box .htaccess file with the current installation.