The Done button causes FreshStart to execute the currently selected environment. If the environment has been changed since it was selected, you will be asked if you want to save or discard the changes to the environment. If you choose to discard the changes, they will be used for the current boot, and will not be used thereafter. This allows you to test changes for a single boot. It is important to notice this behavior, though; discarding the changes does not affect the current boot.