Webtrends Analytics 9 Adminstration Guide, November 2012
Because URL replacement is performed before analysis, your URL search and replace definitions affect the entire analysis for the profiles in which URL search and replace is used.
Unlike URL Rebuilding, URL search and replace replaces any kind of string in the URL, not just parameters, and affects all your reports for the profile, not just reports on pages. Because it affects all reports, make sure you use this feature carefully. Do not replace data in a URL if you want to use that data in any Webtrends Analytics 9 reports.