In the popular novel The Da Vinci Code, written by the American novelist Dan Brown, it is claimed that the earlier Louvre version contained hidden symbolism which contradicted orthodox Christian belief, notably the fact that Jesus is shown praying to John rather than the other way round (the novel implies that the baby at the left must be Jesus rather than John, because he is with the Madonna). It is also claimed that the Virgin appears to be holding an invisible head and that Uriel appears to be "slicing the neck" with his finger. Allegedly, for this reason the painting was rejected by the Church, and a second, more orthodox, version was painted.
There is no historical evidence to support any of these contentions. The only significant compositional difference between the two versions (excluding the later addition of attributes) is the fact that Uriel no longer points. However this difference may well be explained by the possibility that the distinction between Jesus and John was thought to be insufficiently clear in the earlier picture because John is with the Madonna, and that the pointing gesture directed too much attention to John.
Indeed far from the painting being "too scandalous" to show in a church, Leonardo and de Predises actually wanted more money from the church than had been originally agreed. The church agreed to pay a substantial bonus but not as much as Leonardo and de Predises wanted. So Leonardo and de Predises sold it to a private collector and then made a second copy (arguably a superior one as it turned out). So popular (not scandalous) did these paintings prove that it is believed that they painted a third version which is now lost.