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.