I think you would have a higher success rate if you used a sterile technique during these experiments. For example, every time you wipe the tweezers on the towel or your hands you are getting a ton of bacteria on them and then re-introducing it to the embryo. Bacteria can be incredibly harmful to a developing embryo because they have no defense to protect themselves against it. In an eggs case the shell is the protective barrier, but without it, they are left vulnerable. I suspect if the embryo in the Emu egg was still viable at the time its shell and membrane were removed it probably only has 48 to 72 hours before it succumbs to bacterial infection.