Aperture stuck relocating a master (original) file that is not there.

While relocating original files, Aperture stops on a certain file or two that it thinks is there. When I search for the exact file, it does not exist. The issue is on files that are usually named with a number at the end for duplicates or copies like DSC_1234 (2).NEF. I have had corrupted cameras, memory cards, bad memory card readers and new MacBook Air issues so I will admit my Aperture library is probably not incredibly stable. I have rebuilt it using the Command-Option dialog and this issue still persists. After this I will be exporting projects out of this library and start a new but was wondering if any one had any solutions in the mean time?