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From: Richard Stallman <rms@gnu.org>
Newsgroups: gmane.emacs.devel
Subject: Re: Documentation for custom-file - is not (load custom-file)
	needed?
Date: Tue, 07 Dec 2004 23:40:17 -0500
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    Deleting them from the old custom file is definitely not always going
    to be desirable.  It usually will be if the old file is .emacs, but
    not if the old custom file is .emacs-21.3 and the new one .emacs-21.4.

Perhaps it would be ok to the user whether to delete them. 
Otherwise we just have to warn the user about the issue, as
I think you recently proposed.