I could probably handwave it away by saying it has something to do with the quantum signature of her body overall that is a stronger driving factor than the molecules in her body. Where’s Andre Bormanis when you need him to concoct some sort of “tech the tech” reason to make it make sense?One of the reasons this is box-of-hammers dumb is because 98% of atoms in a human body are replaced in a single year. So even if Georgiou's molecules want to go "back" they are mostly elsewhere already.
Of course, even losing 2% of yourself is a big deal. And chances are many of the atoms which we keep over the longer run are in our neurons, since they don't regenerate in adulthood. Which might explain the mental issues she has been having.