Snake eggs are gas- and water-permeable, so anything water soluble can penetrate the shell and expose the occupant to potentially harmful chemicals. Some say that a water-soluble marker like those for children is harmless; I haven't seen any scientific data either way on this, so I err on the side of caution. Sharpies are called "permanent marker" but there are things which can partially or completely dissolve their inks.
Here's a link to an article about some of the potential dangers of Sharpie-type inks to humans. It's logical that these dangers could be magnified in a developing embryo of any species.
https://www.thoughtco.com/sharpie-tattoo-safety-3975986
When I started breeding the standard wisdom said to use only pencil... Using a pencil is still absolutely the safest option. (Of course, one shouldn't use a super-sharp pencil which could scratch the shell.)
Again, I'm so sorry for your loss. I really hope you get a healthy baby from your girl's remaining egg!
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