IMO there's no way Bowerman has only just started to doubt the parents' story. I think he stood up for them in the media because he didn't want to scare them into lawyering up and not co-operating.
LE told the press that Lonzie Barton's mother was cooperative and truthful too, and it turned out she'd lied to them from the very beginning and they knew it (she denied even knowing Ruben when they first told her her son was missing).
The more interviews the parents have given to LE, the more they have changed their stories, the more evidence there is against them. Whereas if LE had named them as suspects right away they would have just clammed up immediately.
Remember Bowerman saying they searched the vehicles at the campsite, then they searched them again and again to make sure they hadn't missed any compartments or something... IMO they thought DeOrr's body might have been hidden in the vehicle by the parents. I don't know, but perhaps a cadaver dog hit on the vehicle after all, and LE have decided not to make it public.
Moo.