If you don't know about the rating or keyword filtering shortcuts in Aperture, you may unknowingly press one of the keyboard shortcuts that invokes a filter, and then wonder why some or all of your images have disappeared. Don't worry. They're not missing.
If you don't have any images tagged to a particular keyword, Aperture won't display any images when filtering for that keyword. The same is true for ratings.
Tip: Filters treat stacks based on the pick only. If your pick is a 4★, but you also have a 5★ in the stack, the entire stack will be missing when filtering for 5★.
If you're concerned about your "rejects" specifically, remember that the default filter of "unrated or better" hides your rejects, which are considered to be a lower rank than "unrated."
To see "unrated or better" images again, you can just click the "x" in the search field to clear it. To see all images, including rejects, simply press Control-` (accent grave, same key as tilde); or click the magnifying glass icon to access the Filter HUD, then deselect the keyword criterion.
Note: After you invoke a filter, it will persist until cleared, even after selecting a different project or quitting the application.