I think it just overwrites the original install components - nothing is duplicated.So i installed the 10.10.4 update thru the app store first and had problems with mail & game center... so them i installed it again using this link, the combo updater. did i install the update 2x? did it over right the original install or make copies of each? The combo fixed things i think, but i still had to manually change some of the system app icons b/c they were blank
I think it just overwrites the original install components - nothing is duplicated.