this is kinda my fault for not focusing on the instructions, but the upgrade packange comes with index.php (the default for /install directory) which is the install script for the forums. this can actually clear the forum database if run...
might i request that page not be included in the package?
err.. /install doesn't clear the forum database unless you actually run it past the database config step. Why would you 're-install' your board if you've already installed it? The MyBB update is there for all the 'updated' files between the previous version and the current version, everything is included.
His point is that the install/index.php shouldn't be provided for a changed-files set which assumes MyBB is already installed. install/index.php should not be needed in an upgrade anyway as install/upgrade.php is supposed to be used.