Hi Janie,
> When you federate the server to the Portal, it copies your rest services into Portal.
This statement is not quite correct. After you federate your GIS Server with Portal for ArcGIS, its web services are automatically registered with Portal. They are NOT copied to Portal. When they are registered, there are now discoverable in Portal and can be easily found.
Now you have the option to access the GIS Server's web services via their REST endpoints (as you would before you federated with Portal via the Services Directory) or by accessing their individual Item Details pages in Portal. Keep in mind, by default - after you federate the GIS Server, its web services are still public - but permission access could be changed later on.
Hope this helps,