I am doing a clean sweep of my files. I originally put them in the root directory (don't say anything :-), but am putting them over to a folder named Websites in My Documents. Then within my new folder, I've copy / pasted from the root directory to it and the structure matches.

When saving files like Photo Gallery or Jukebox, I've always saved under Music or Photo Albums. Those were moved to the new site with again, the same tree structure.

So, what am I doing wrong when the new upload knocks the .xml files from the site? I have to go through and rebuild it back in the vnu file (steps - remove files, save, import .xml file, save, etc).

The project files are looking back for the original file locations. What would have made things easier would have been to create the new direcory structure first, then open your xml files for all your CC projects then save them to the new file locations. After that move the data from the original directories to the new ones.

So the copy / paste of the what - 3 or4 files - from these programs is a mask, and they should get the original reading with a fresh Save As? I will give that a try, but I don't understand the reasoning behind it. I started off with DOS on the 88 machines and my thinking still follows those procedures

Windows doesn't follow any procedures.