The scripts documentation [1], where flatten.php is mentioned, states that flatten.php will reduce the version count for each object to DefaultVersionHistoryLimit. This is wrong. This script has no knowledge of this directive, and will instead remove any non-published version, leaving only the one with the PUBLISHED status.

This has to be fixed, as flatten indeed removes LOTS of versions.

1. http://ez.no/doc/ez_publish/upgrading/the_system_upgrade_scripts