Here’s the problem. Whenever you enter search terms into the box, they stay there until you erase them, which makes it pretty easy to think that some of your photos are gone.
Even if you shut Aperture down and reload it, those search terms will remain there, and that means you’ll only see the photos that relate to those keywords.
This was a real problem for when I was a beginner, because I would open my street photography project and only see my Brooklyn photos, or my Manhattan photos.
So if you think you’re missing your photos in Aperture, you’re probably not. Check that search field!