Soleil has it. Under the JAA when your pregnancy is confirmed you inform your employer and the medical certificate immediately lapses. It is re-instated following an examination by an AME to ensure there are no complications and is subject to continuous review so that if, for instance, morning sickness developed it would be suspended once again. The pilot can fly until the 32nd week.
Employers have an additional requirement to ensure that cosmic radiation dosages are kept as low as reasonably achievable and not exceed 1 millisievert in the remainder of the pregnancy. Some employers (BA) prevent pregnant women flying as pilots or crew on that basis.
If a women is unable to fly because of her pregnancy she must be found suitable alternative work. Maternity leave rights for pilots are the same as for the rest of the working population.