Assuming you mean when writing to the scanner...
The system files that you have checked will be written but the configuration file will not be written. So no new information will be includeded in the radio configuration but you will have new systems based on the checked ones. Also, you didn't ask, but please note that you can have duplicate systems in the radio. Lets just say you updated a system (call it "XYZ") on the computer and then wrote it to the radio. Assuming you already had an "XYZ" on the radio, you then would have two "XYZ" systems on the radio.