Global Colors issue, in Adobe Illustrator CS 3/4

Question

  We have this issue where I work of colors remaining in swatches even when deleted, which for some reason creates huge files when saved, 1 gig + at times.
  The colors that remain in the swatch are all titled "Global Color", it is possible to select and delete them all, but it is just an illusion, as soon as you copy and paste anything from the document all the Global Colors return.
  I have browsed the web and seen no solution to the problem. I have many files infected with these colors and can upload a file somewhere for any one to investigate.
Thanks.

Answer 1

Same problem here. Any copying and pasting between documents spreads this. Here is what I have tried so far that has not worked
Recovered the file using 'Content Recovery Mode = 1". Edited this in simpletext to remove all code that has "Deleted global colors" & the "Begin PluginObject: Object". There was lots of junk to remove and I got everything in between the open & close tags.
Saved files as AI3
Copied & Pasted all elements into a new document
Removed all unused Brushes, Swatches, Graphic Styles
Removed all layers & did a save as, the file is still 6mb with nothing in it.
In my situation, 1000s of brushes reappear in the library(see images below) after any copy/pasting. I also had "deleted global colors"(see images below) reappearing but that has gone away since I cleaned up the code. The problem must lie in in the non-standard characters. I also am getting the HUH error(see images below) when saving. I stopped getting the swatch conflict error(see images below) after pasting, after I cleaned up the code. The file though is still huge, slow and any copying is really slow. Can't load CS5 trial here at work(to try out that new cleanup command), but am on CS4 Mac.