Hi Seth,
The female will stay with the eggs for another day or so after laying is finished. Then they'll come out for good. When the females are finished laying eggs (and during laying) they are in kind of a semi-comatose state. They have no inclination to leave until their heads clear up. Yanking them out of the egg box tends to get them back to reality pretty fast (and it is pretty disturbing to them as well). In captivity (and in the wild) Eastern Indigo females won't revisit or stay with their eggs. Once the embryo has floated to the top inside of the egg (several days) the eggs can't be toppled or rotated so it is disadvantageous for the female to be interacting with them. Chicken eggs need to be rotated but this will kill Indigo eggs.
I remove my females right away because I need to check them for eggs still inside them. Usually these are slugs. If you get to the female late in the same day that laying started (laying usually starts at or before sunrise like you mentioned) then any slugs can usually be manually moved out easily. Females don't seem to have the urge to pass slugs like they do fertile eggs.
You are having remarkable fertility results. Congratulations.
Robert Bruce.

