It's like there is a ghost version/image in the original project that I can't seem to clear.
Have you checked if you have invisible photos because you rejected photos? Is the "rejected" album empty? Are all search fields cleared, also for the project with the invisible photo? The search fields could have a filter applied to the project or the Browser. Can the image in question be edited or exported, or could the original master file be missing?
Is it possible, that you accidentally copied your photo to the other project instead of moving it there? Usually dragging an image to a different project will remove it from the original project and move the image and all versions to a different album. But there is a glitch in Aperture, that Aperture will create a duplicate image and add the copy to the destination project, if you hold down the options key while dragging the photo. But you should be able to drag this copy back.
if there are no filters and hidden photos, and the photo can be edited, it might be a library corruption. In that case make a current backup of your library and repair your Aperture Library. See this manual page: Aperture 3 User Manual: Repairing and Rebuilding Your Aperture Library
