It has never been considered good practice to manually alter the contents of the Aperture library in the Finder. In Aperture 2.x and later it is especially important to avoid manual changes within the Aperture Library. Make all changes to your library from within Aperture, whenever possible. If you experience issues with your Aperture library, restore it from a recent backup, if one is available, or rebuild the library by holding down the Command-Option keys when starting Aperture.