Most if not all of my 16,000 images (and videos) I access in Aperture are “Managed.” Most of then, over 60 percent, came into Aperture via an import from an external hard drive, and the remaining files came in to Aperture by transferring the photos directly into Aperture from my cameras.  My problem is that I would like to reorganize and bring sense to the structure of the external drive where many of my photos originated. Especially so since Aperture’s days are numbers. 

Currently, the images in the external drive are in a confusing mess of folders (and sometimes folders within folders) that contain many duplicates and even renamed and re-dated (!!!!!) duplicates. (Luckily, I do not use this hard drive as the one which I backup my iMac through Time Machine).

How should I go through reorganizing and moving the photos in this external hard drive without screwing up accessing them by Aperture, and later Lightroom and other photo programs?