The Apply button does not work properly in the Phasing dialog. If you make some edits, select the Apply button, and later cancel the dialog, the changes you applied are discarded. This is not typical behavior for the Apply button.
Per MS UX guidelines, using the Cancel button will discard changes made after the last time the Apply button was used.
Most of the rest of Revit's UI has the correct behavior for the Apply button.
Please correct the behavior of the Apply button in the Phasing dialog. Reference case # 13955670.