I've never tried maternal incubation, but if I don't see them right away, then they start looking deflated like that, I'm pretty sure it is due to loosing water. I then put them in an incubator, but then really don't see them plump up more.
I have had eggs much worse than that hatch out though and be fine.

If they start turning colors, or leak, then they are likely bad, but I wait until it is VERY obvious before removing anything just to be sure.