It would not hurt to see if you can transplant or pull them out and fix your issue... it is worth a try....or just transplant them...
Are you using coco and/or airdomes bro? I wouldn't worry about not having the bottom layer of pebbles if you are... If not then might want to repot.
I am using clay pebbles, coco and perlite. I just attempted to transplant them and the coco was too loose. I was just left with giant root balls. I just took everything down and had somewhat of a cleaning fit. 4 new surprise seeds have been dropped and I will update very soon.
I re-potted my AutoPots with a 1" layer of clay pebbles around the Air Domes, and the rest coco/perlite.
i guess at least you didnt get half way through the grow and something bad happen to them like this... best of luck on the next ones! ill be watching for it!