Major Description
This happens any time initMavenPlugin is called after the creation of a custom portal's project.xml or if the the maven plugin's project.xml has a newer timestamp then the custom portal's project.xml. Even though the overwrite on the copy task in the plugin has overwrite="false" this does not help the case when the plugin's project.xml has a more recent timestamp. All the overwrite="false" does is force the copy command to respect timestamps, which it does do. However, this does not prevent the maven plugin's project.xml with a newer timestamp from overwriting the local project's project.xml.
A check needs to be put in place to prevent the copy based on the prior existence of a local project.xml.