Any of the below should do:
# 1.
children = session.query(Child).filter(Child.parents.any(Parent.id==??))
# 2.
children = session.query(Child).join(Parent, Child.parents).filter(Parent.id == 99)
# 3.
my_parent = session.query(Parent).get(2)
children = session.query(Child).with_parent(my_parent).all()