I'm on my first time incubating with an incubator. I've hatched tons with broody hens. So I can't answer that, about the leaving them in there. I read some people pull chicks, some leave them. So I think it is more your call on what to do. If it was me, I'd pull chicks if there was a bunch dried...
I think, if you have a handful of chicks dried/fluffy and moving about, you could quickly pull them out. And just keep watch on your humidity and temps afterwards. As for the mishaped chicken. What kind of chicks are you hatching? Silkie, polish and I'm sure other out there have vaulted skulls.