From EW’s Spoiler Room:

Are we done with the Bracken storyline on Castle? — John
If I had to guess, I’d say not so much. Showrunner David Amann says that although most of the storytelling surrounding Beckett’s mom is done, there is a “Bracken-related storyline that presents later in the season.” “We like Bracken as a character,” he says. “We think he’s an interesting person to access and there may be a reason moving forward to go back to him again.” Now the question is: Does it have to do with Castle’s disappearance?