If a WebLogic Application is installed using the N1 Service Provisioning System 4.1 and then content changes are made to the on disk WAR archive on the administration server, the changes are not reported in comparison results. The problem does not occur when configuration changes are made.
Workaround: Comparisons can be customized using the generate and prepare extensions with more capabilities to pre-process the on disk representation prior to running the comparison. This may require some advanced scripting.