The module doesn't delete configuration data at all. There are several items around security which must be addressed. Users upgrading to module version 4.4 should first mark their forum pages as admin only till they work through the configuration changes. The most important change is going in and removing edit permissions for each module instance for Registered Users and non administrators. Once on the module settings, administrators should also add the other permissions available after the module is installed. Next, administrators should go through all the control panel pages and verify things are setup as they would like them to be.