That's a good, and potentially non-obvious, question. This isn't a case of photocopying a manuscript for presentation purposes (which I never do). Rather, the significance of photocopying the CEM (copy edited manuscript) of the novel is twofold:
1) The corrected (by me) CEM is the final version of the book as it will go to the typesetter. By keeping a copy, I am able to respond quickly and accurately to queries during the typesetting and production process. This could be anything from them not being able to read something in my crappy handwriting to a request for clarification on a note from copy editor that conflicts with a note from me. Otherwise Tor would have to fax or express mail me a copy of the page in question for review, which takes time, trouble and money for all concerned.
2) The corrected (by me) CEM is the final version of the text of the book, pending changes on galley, which will be typographical only. In the future if I were to sell overseas rights, or rights to some other edition, I need to have the finalmost edition of the text of the book. If I simply went with my last electronic version, it would be pre-copy edit, and thus lack literally hundreds of changes and corrections which currently exist only as handwritten notes on the CEM, either from the CE or from me. If I were feeling diligent, I'd create a new electronic file on my hard drive with those changes folded in. Right now I'm too busy to stop and do that, but keeping a copy of the CEM gives me the means to do so should I ever need to.
I'm sure other authors and editors can offer their own observations on this process, but that's my two cents' worth.