Would the police take my other child if one child is taken due to medical neglect?

I cannot answer your other questions if you don't say what they are. As to losing custody of the other child, while it was a possibility, if by winning your case you mean that a court has ruled that medical neglect on your part has not been proven, it is far less likely that the authorities would try to remove the other child. It remains a possibility, but they will likely conclude that they have other fish to fry.