When you perform a Web Crossing upgrade or "reinstall", none of your data or design is changed. The only exception is the IMAGES and WBChat directories. New versions often contain new graphics for new functions as well as updated chat applets. So if you have changed the default web crossing buttons, make a safe copy of them to put back after the upgrade is complete. If you've customized and recompiled any of the JAVA chat applets then you will want to have a copy of those too.
Note: upgrading to version 5.0, which is a major change from previous versions and now includes plugins, built in themes and extensions, etc, may need tweaking in order to not conflict with your existing customizations. You mayalso find that previous customizations are no longer needed as they are build into 5.0s extensive options.