Ok so I spoke to soon. I checked the queen cells yesterday and they were all dead/not there. There was several cups that looked like they had started building queen cells and two queen cells fully built but had a hole in the side of them with bees going in and out. I guess they died. I checked the hive for other queen cells before but maybe I missed one I only saw the one original queen in the hive.
I took the hive which was a 2 deep hive and took all the eggs and young larva out with the queen and put them in another box and moved them to a different bee yard. I left all the capped brood (so long as it did not have eggs or small larva on the frame also), some open honey, pollen and capped honey in the original hive. So now I have a queen less hive that should be pretty packed with bees. I am going to graft into it again tomorrow hopefully it will turn out better this time.