When performing a SVN update, you may be safe deleting your character config. file only because if there is any changes made to the file it will now be added in. Unless you know how to add it in yourself and look through revisions then you are best off with a fresh start. Now this is only if you see that there was a change to a character config. file not for every update done.
So example time..
Ok time to delete my file and re create character config in order to have the update added or search the revision change log and add it in myself.
Ok this is a merge update, only need to search what the revision was so I know what it was and if it affects my settings I already have, if I even care what it was about.. don't delete it.
You could give winmerge a try (I haven't messed with it myself tho).
Also, in case your runs don't change and you don't need any of the new features, you can leave the configs intact (defaults are always in Config.js so at least you won't get any errors).