Photos replaced iPhoto.
Nothing replaced Aperture.
But this replacement took place only in the Apple product line. Neither app is sold or developed any longer. However, both continue to run on current OSes, in their most current version.
The change did not happen with Yosemite. Development ceased on Aperture and iPhoto about a year before and the Photos app wasn't released until the third iteration of Yosemite - 10.10.3
No machine with an existing install of Aperture or iPhoto had anything replaced. They simply had Photos added to their suite of Applications. The move from iPhoto (or Aperture) to Photos is always a user choice.
The original poster has used both iPhoto and Photos, as he says. So, I'm not really sure why you're point is. In the meantime he or she has a serious issue on their machine - apps disappearing. Do you have anything to contribute to that?