Although delving into multiple concepts, this tough question can be coincidentally fixed on the
D-day by the correlative conjunction parallelism of –
not to … but to --- about which Mike has pointed out.
(A) that the Roman Catholic Church formally proclaimed in 1854,
not referring to the conception of Jesus, which, according to Christianity, occurred miraculously despite his mother Mary being a virgin, but to the conception of Mary in the womb of her mother, Anne, despite the fact that they believe this conception occurred with --it should be
referring not to the conception …. but to the conception. (B) that the Roman Catholic Church formally proclaimed in 1854,
did not refer to the conception of Jesus, which, as Christianity says, occurred miraculously even though his mother Mary was a virgin,
but to the conception of Mary in the womb of her mother, Anne, despite the fact that this conception is believed to be occurring by—correct format is –
did not refer to the conception but referred to the conception
(C) of the Roman Catholic Church formally proclaimed in 1854, referring
not to the conception of Jesus, that in Christianity occurred miraculously with his mother Mary being a virgin,
and to the conception of Mary in the womb of her mother, Anne, despite the fact that this conception is believed to have occurred in ---
use of ‘and, takes away the contrast and is unidiomatic. – It should be
not to – but to-- (D) of the Roman Catholic Church formally proclaimed in 1854, refers
not to the conception of Jesus, which, according to Christianity, occurred miraculously even though his mother Mary was a virgin,
but to the conception of Mary in the womb of her mother, Anne, despite the fact that this conception is believed to have occurred by ---
correct idiomatic parallelism. (E) of the Roman Catholic Church formally proclaimed in 1854, referred
not to the conception of Jesus, that, as Christianity says, occurred miraculously when his mother Mary was a virgin,
and to the conception of Mary in the womb of her mother, Anne, despite the fact that they believe this conception occurred by ---
same error as in C