WebSphere Portal 6.1 depends on Virtual Member Manager (VMM) for security. The VMM configurations are applied at the cell level and maintained at the Deployment manager level. When you federate a node into the Deployment manager it wont change any of the deployment manager security settings instead any changes that you made at the portal level will get lost and portal will inherit the security settings at the Deployment manager level.
Note: If administrative security is deselected during installation of the deployment manager or is disabled after the deployment manager is installed, it must be enabled prior to executing the security configuration tasks on the WebSphere Portal cluster members.
WebSphere Portal provides a number of security tasks, which can be used to modify the WebSphere Application Server security settings and make the required updates to the WebSphere Portal configuration in a single step. As soon as a WebSphere Portal node is federated into a deployment manager cell, all WebSphere Portal security tasks will execute on the deployment manager. Run security tasks after federating the WebSphere Portal node because the Deployment Manager cell does not contain the configuration resources required to run the security tasks.