Originally, there was just one WGN. Once WGN picked up a network affiliation (that was the WB and is now the CW), they had to send out a second signal with alternate programming to viewers outside the Chicago area since network programming would be blacked out in any location that had a local CW station. Eventually, the two stations diverged to the point that the only common programming was Bulls/Sox/Cubs games and the evening news.
WGN America (which is what everybody outside the Chicago metro area gets) has decided to stop showing Cubs/Sox games, so they will now only air on the local version of WGN.