Hello Jean-Pierre,
If I'm understanding you correctly then this is not limited to the setting that you mention.
For example, if I set authentication mode to "Forms" in Application Designer the config file for the implemented app will show that setting as "Forms", even if I include that app in a System and override the setting to "Windows" in System Designer. (note that if I change the setting to "Windows" back in App Designer then the config file will update accordingly).
If you go on to create a Logical Datacenter, deploy your system to one of the LDD servers using Deployment Designer, then generate a Deployment Report you will see the overridden setting in the section of the report relating to your System. In other words, if you override app-level "Forms" authentication to system-level "Windows" authentication the deployment report will show "Windows" authentication.
Tony Loton
"Professional Visual Studio 2005 Team System"
http://www.amazon.com/gp/product/0764584367
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