This is a little sad piece of Church history and it’s about babies, so some folks here may not want to read this post.
Okay. The reason that the Church does not baptize embryos or attempt to baptize children still in the womb. Turn back now.
Back in the 1600’s-1700’s, as scientists and priests got more interested in the mechanics of babies being born, some very pious doctors and priests thought that it would be a great idea to baptize babies before birth – because after all, it was fairly common for many babies to die during birth.
What they found out was the same thing people have found out every time when this is tried, back in early Christianity and still today. It is very very difficult to baptize a baby in the womb in any way, no matter how careful, which will not cause miscarriage, drown the baby, cause interior infections in the mom, etc. Death rates for both mom and baby go way up.
So there is a rule in canon law that the Church does not baptize babies until they are all the way born. We just don’t.
If a baby dies before he can be born and baptized, then there is such a thing as conditional baptism.
But whatever happens, that is the Lord’s decision; and we should trust that God can take care of His own in these cases. We also have to trust that the Lord Who counts the sparrows knows all about what should be done for frozen embryos, miscarried babies, and aborted babies, better than we do.