My guess is it was fuel/weight related. In Comp Eliminator, you still have to submit fuel and weigh in after each round win. In crash situations, NHRA usually has a little bit of forgiveness/wiggle room. For example, when a fuel funny car wins and grenades the motor in the lights shredding the body into a million pieces, they don't require the team to find all of the small pieces to weigh the car in. They weigh the car as is and add the amount of weight the body would normally be.
I don't believe Brogdon is in a full out chase for points or the championship. If this is true, and his car was on a flatbed trailer, I'm sure he wasn't in any hurry to either submit fuel or attempt to get it weighed in. If we know for sure he wasn't DQ'd for excessive braking, then my guess is he told DePalma he wasn't going to submit fuel or weigh in as a gesture of sportsmanship since he was done for the day, or, he was so angry about the crash, he said, "F*** it, I'm outta here," which led to him being DQ'd and DePalma reinstated. Again, just a guess, I don't have any first hand knowledge of the situation.