That is probably fine.
If you have changed any of the configuration files it is likely a very good idea. I have very carefully changed a number of the scripts used in grub for instance. /etc/grub.d/05_debian_theme is one example. This is changed to make the font color of the screen menu work with the screen menu background that I have put in.
Another common config file that you get that question with is when bash is upgraded. This question will have to do with the .bashrc. If you have not changed it there is no harm in upgrading the file. If you have used it instead of the recommended .bash_aliases to have a custom alias then you will loose that alias if the file is changed to the new default.
There are a number of those questions, however, that I think you should probably let the installer change. If you have not changed them the upgraded wording may work better or be needed for some upcoming change in the application that the config file controls.
Indeed I have had to, after a couple of years of using the same 05_debian_theme file had to upgrade to the developers new file so that it actually would work at all. There were several lines added that just had to be in there.
Basically if you have not changed the things yourself it is best to keep the files up to date. In most cases you will never see any difference in look or performance. They may just be a cleaner version or a security update.
The ones you have changed you should have saved the original and your edited version to some backup directory and if needed you can get the new version and then redo your custom edits.
Dell XPS 420 Core2 Quad Q 6600, audigy5.1, Radeon HD 6450 - currently 4 320Gb HDD, Debian Squeeze for secure use, Debian testing for daily use, Debian Sid for fun.