Licences do not move automatically when a USB eLicenser is connected - you have to drag and drop a licence manually in eLicenser Control Center to move it to a USB eLicenser. You can move licences freely to and between USB eLicensers. Moving a licence from a soft eLicenser to a USB eLicenser is a one way operation: you cannot move a licence from a USB eLicenser to a soft eLicenser.
If you want a Cubase Elements licence to have a DAW without your dongle, you need to activate Cubase Elements on your soft eLicenser. Arguably the best way is to disconnect your USB eLicenser when activating Cubase Elements so that you cannot accidentally activate Cubase Elements on the USB eLicenser. That said, if your USB eLicenser is connected when you attempt to activate a licence that can be activated on a soft eLicenser, you should get a dialog asking you which eLicenser you wish to activate the licence on.