When you say "catalog" I think you are writing of using the Organizer that comes with Elements. If this is not the case, then please provide more information.
The photos, scans or those from a camera, that appear in the Organizer are only thumbnail representations of your actual photos. What you are seeing with the Organizer are not your photos. The Organizer is a database program that is keeping track of your photos and where "you" put them, not Photoshop. If you want to continue to see all of them in the Organizer, then any moving or deletion of the actual photo file must be done with the features of the Organizer.
If you are not using the Organizer or do not intend to, then you can easily copy, move, delete with Windows Explorer. If these scans are jpg, then you can use them in other programs just as is. Perhaps the same is true with bmp format images. These other programs would include email programs, Paint, Paintshop Pro, GIMP. Only if the scans are psd or tiff files will they not open with other programs.
If they are psd or tiff files, Elements has a feature that will change all 1,000 rather quickly. In the Elements Editor, File > Process Multiple Files and there you can do a number of things. Look for yourself as there is not enough room to outline all. My suggestion would be to always have a destination folder different than the folder that contains you scans. You do not want to wipe all your work out by a stupid mistake.