I use Ubuntu, but your question about Kali OS is very like those I had when I was introducing to it. I think the answer will be common for any Debian-based distributions. Look for such entries in your
# deb cdrom:[Ubuntu 13.04 _Raring Ringtail_ - Release amd64 (20130424)]/ raring main restricted
Do not pay attention to the name I provided. Your will be different. Just notice the syntax of this entry. If you want that software in this repository to be included into update alternatives, simply remove hash sign. But this will not provide you last updates or even large repositories because CDs are usual used to install software initially, not to update it.
UPD: If what do you need is only to restore software came from DVD and not involve Internet in any part, then you should comment out all entries that have URL's like
# deb http://example-link.com/mirror/distro releasename repository1 repository2
and retain only
cdrom entries enabled, then run:
mv /var/lib/apt/lists /var/lib/apt/lists.old
This will give you options to install software using original DVD, but sooner or later you will discover that it is not enough. Also you did upgrade, so you will have to deal with unmet dependencies. Possible solution is to downgrade all involved packages, but I strongly recommend you not to do it.
What is really useful that is mirroring. When you have slow connection on one computer and rapid on another, you can use rapid Internet connection to build mirror then deliver this mirror to "slow-or-expensive-Internet" computer. This guide covers first part completely. I just recommend you to stop before creating DVDs and use portable HDD to hold the mirror. When you connect your storage to computer you wish to update, create entries like I have in
deb file:/media/Elements/UbuntuMirror1/Ubuntu precise main restricted universe multiverse
deb file:/media/Elements/UbuntuMirror1/Ubuntu precise-updates main restricted universe multiverse
deb file:/media/Elements/UbuntuMirror1/Pidgin precise main
deb file:/media/Elements/UbuntuMirror1/VirtualBox precise contrib
Sorry for Ubuntu-specific release names and all related stuff. I just took them for example. You can change 'precise' to 'wheezy' or Kali-specific release name. But I must state that
apt-get works most unified on any Debian system so I hope my tips will be helpful. And keep in mind that if your Internet connection is not slow, not so expensive and if you do not have another computer with really fast Internet, the best way to update system is following default procedures.