Good news! My newly installed queen is doing great, and I actually saw her!
Here’s the problem. The new split I did last Saturday, so six days ago, only had about 50 to 75 Bees in it. There were no queen cells, the uncapped brood was still uncapped and the capped has not hatched. There were some open brood that I could see the larva and it was like they had been opened up from the outside if that makes sense. But they hadn’t matured. So here’s my question. Do I add these frames into the original hive? There’s only two but there’s also a couple frames of pollen and nectar.( or uncapped honey I really can’t tell). Or can I freeze those and give them back to my hive later (not brood, the pollen/nectar). The capped brood that were “opened” concern me a little bit. Why would that be? I took out the few bees that were in there and I’ve closed it up for now. Thanks in advance for any advice. Oh and they’re storing and capping honey up in the flow!! YIPPPPEEEE!!
Just making sure I understand, you saw this now when you inspected? And 6 days ago when you made the split there were more…
And no apparent progress with the existing cells of brood…I would guess that the workers drifted back to the original hive.
Were they worker or drone cells? Did they look like formed bees that were all white? Or an earlier stage/worm? I’m not sure why workers chew open caps from outside except when they have ‘hygienic traits’ and know the brood is diseased or infested, and then they would remove the brood and dispose of it. But of course there haven’t been enough hands on deck to finish this job. My concern would be varroa, but I doubt there was a mass die-of from it.
Assuming you put these back into the parent colony? So you now have just the one, with your new queen.
Yes - freeze and store the honey and pollen frames for another day is what I would do, unless you are tempted to start another colony and give them to a package or nuc 
And wow, yipeeee indeed for your Flow super getting filled!!! 
Yup definitely more bees and I really tried to include nurse bees on the brood frames.
I put the small amount back in the original hive. Other than the large larvae stage open brood (and I’d say 6-10 not all and a few were drones
), there are no signs of disease. But I don’t know if I want to take a chance and introduce them back into the hive if that is the case. If my math is correct, capped brewed will hatch in another five or six days so maybe I’ll just go check it then and see if they do, I don’t know what else to do at this point. I think I will freeze the one or two frames of pollen and nectar.
Ok so… I just went out there, and there are quite a few bees flying around the split obviously trying to get in. So I’m thinking it was such a nice day today there might’ve been quite a few foragers from that hive. I flipped the excluder back to open. The only thing at this point is if they get going and those eggs hatch, I’m going to have to get them a queen.
I think I’m going to do a just in case mite treatment. Because those frames came from the original hive I just want to be sure.
A photo would help with this, but I agree with @Eva, if your bees are a “hygienic” strain, varroa is the most likely reason. But also, if there weren’t enough bees in the hive to keep the brood warm, they die in a day or two. If the larvae and pupae were dead, the bees would want to remove them. Dead brood smells pretty bad quite quickly, and bees are very sensitive to aromas. By the way, technically if the cells were capped, that was a pupa not a larva. Bees only cap the cells when the occupant is ready to spin a cocoon. At that stage, it becomes a pupa.
I would not add those brood frames, in case it was the smell of dead brood that made the bees leave. You don’t want your strong hive to abscond at this point… 
By all means add the honey/pollen back, if there is space for it. Otherwise freezing it would be fine, as @Eva said.
It is great that your hive has no queen cells, and now they are filling the super. Congratulations! I know that this has been confusing, and a bit of a rough ride for you, but I am sure that you have learned a lot. 
I agree-I’m not going to add the brood frames back to the other. Im going to do a precautionary mite treatment on the original and freeze the 2 frames with nectar and pollen stores from the split. Any suggestions on how to clean or just get rid of the brood frames with questionable open brood? Without a queen and possible mites, I don’t think it’s worth trying to salvage.
I would render them for the wax. You can freeze them until you have enough to make it worth while. If you use the magnifying glass at top of the page, you can search for crock pot or slow cooker rendering of wax, which is my absolute favorite method