How old were the pictures that are missing? Since the Photo Stream servers only maintain pictures for one year, when you copied everything back to Aperture, it probably would only pickup up the more recent (read less than one year) photos that are still on the server. I went through this when I had to replace my iPhone 5 and when my wife got her iPhone - it did not show the older photos.
You are probably seeing them on the Apple TV (I am not sure because I don't have one) because those photos are probably stored on the device itself - like the photos are stored on iPhones, iPads and Mac hard drives.
many of them were not even 4 months old. as a whole set. Like the one from my sister-in-law for example. her whole set disappeared in Aperture. But it is still visible on my iPhone.
The AppleTV does not have internal storage other than a buffer for loading parts of a streaming movie, or a photostream.