The simplest explanation is that Grand Superme Kai became Mr.Boo.
The elder Kaioshin basically states that by removing the aspect of good that Evil Boo became the stronger Pure Boo.
What was removed?
Mr. Boo.
What was the good aspect?
Mr. Boo
What was the creation of the good aspect?
Grand Kaioshin
Mr. Boo ~ Grand Kaioshin. For the most part... I also think that some aspects of Pure Boo remain inside Mr. Boo along with some aspects of South Kaioshin.
Mr. Boo = Aspects of Boo + Grand Kaioshin + South Kaioshin.
Also I think that it is more of permanent fusion kind of like how after Chou Boo "absorbs Vegito" he decides to take off the Gohan pants. It is because the absorbed will eventually fade away and just be aspects of him.