I would just like to report that mnn's solution works. He got the config syntax wrong, but there is a set method that works for most data types.
I wanted to read in an integer array, then sort it, in order to take advantage of reading this array later in a fast method. So I figured I might as well sort the array and save it back to the config. Here's the solution:
int[] white = config.get("WorldGen","dimensionWhitelistList", new int[] {0}).getIntList(); //read the values, supplying defaults
int[] black = config.get("WorldGen","dimensionBlacklistList", new int[] {-1,1}).getIntList();
Arrays.sort(white); //sort
Arrays.sort(black);
String a=Arrays.toString(white);
String whitestring[]=a.substring(1,a.length()-1).split(", "); //have to convert to a string array in order to write
String b=Arrays.toString(black);
String blackstring[]=b.substring(1,b.length()-1).split(", ");
config.get("WorldGen","dimensionWhitelistList", new int[] {0}).set(whitestring); //default values here are irrelevant, but required in order to retrieve the config Property
config.get("WorldGen","dimensionBlacklistList", new int[] {-1,1}).set(blackstring);