Its definitely possible that Prater has no idea that the BHB still lives.  But, theres tons of ways they could introduce the idea that Prater has believed otherwise. He has lots of connections, he could be in possession of intimate knowledge of the BHB case and have the same doubts that Doakes was the true killer as did others familiar with it. Hell, he could even be directly connected to people involved in Dexters past we just havent learned about yet. I dont think its a stretch that Prater could have reasons to believe it that just havent been revealed to us yet.