I also had EXACTLY this happen -- but the chick also had a splayed leg and malformed foot, which may be why he couldn't finish zipping.
I had 3 of those last year, that had trouble zipping, and, interestingly, all of them died at some point later. One was very obvious - it hatched with severe wry neck and died 4 days later, despite my best efforts. So okay, that one had issues and couldn't zip. With the other two it wasn't so clear. They were very lively and vigorous when I pulled them out. One had an eye problem, and the other was a bit smaller than the others, but nothing too bad and they were otherwise vigorous and healthy-looking. The small one caught up to the others quickly and lived a very healthy life until she dropped dead for no reason at 9 months old. Necropsy showed multiple organ failure and a bad valve in her heart. The one with the eye also caught up and grew well, but kept blinking his eye a bit too much throughout his life. At one point he mysteriously caught and developed mycoplasma (the only one in a flock of 35, which is odd given how contagious it is, so he might have had other, hidden, underlying conditions that made him susceptible?). It gave him crippling joint problems and other issues, and he had to be euthanized at age 1 year, because treatment wasn't helping and his quality of life was so low. I did the necropsy on him, while processing him, because he was always meant to be eaten anyway and if I'd sent him to the vet, he would've been off the table as food. I'm no expert, but he looked normal on the inside - liver looked healthy, heart wasn't enlarged, very good weight overall, no red flags, just severe muscle loss in his atrophied legs, especially the right leg, from not using them because of the joint problems.
There's no way to know if any of that is connected to those chicks' inability to hatch. But it would be too much of a coincidence that out of a batch of 15, those 3 were the only ones that failed to hatch and were assisted, and they are the only 3 that died young... Another observation is that out of those 15, 6 were shipped eggs and 9 were local eggs, and all 3 that had problems zipping and later died, were from the shipped eggs. I've done both shipped and local eggs a few times now, and this is a clear trend - shipped eggs fail a lot, but they fail very late in development. With the local eggs, anything that makes it past the first week, will hatch no problem. Shipped eggs tend to die in lockdown by failing to pip or zip. I'm guessing because their air cells are messed up, or the chick is malpositioned.
