Those are used for the message log. (M key). As you get contact messages the file gets larger and larger, resulting in a longer load time. Starting a new mission starts the message log over again.
I did the change to the radius of notification for contacts and rarely get messages unless they are within 250kms(the default i set). This way the message log doesnt get large.
I will look for the thread and post..
EDIT: Here it is
http://www.subsim.com/radioroom/showthread.php?t=108959
Or manually change the file like i did after you back it up.