In late antiquity, Romulus and Aeneas were finally reduced to the myths they had threatened to become for centuries. Their stories, however, were never forgotten or replaced.

Even in Virgil's time, there was a great deal of skepticism - at least among the elite - about the historicity of Rome's foundation myths. As Livy says in the famous preface of his history:

"Such traditions as belong to the time before the city [Rome] was founded...and are rather adorned with poetic legends than based upon trustworthy historical proofs, I purpose neither to affirm nor to refute. It is the privilege of antiquity to mingle divine things with human, and so to add dignity to the beginnings of cities..."

Likewise, Livy's account of the birth of Romulus (1.4) notes merely that Romulus' mother claimed that her twins were the sons of Mars, and suggests that she may have been trying to conceal an illicit affair. Educated Romans, in short, were free to doubt the existence, or at least the divine origins, of Romulus, Aeneas, & co., and seem to have regarded their foundation legends in the same skeptical spirit as the traditional Greek myths.

Although we have no clear idea about the opinions of the illiterate majority, the Roman elite was generally dismissive of the myths (e.g. Dion. Hal., Ant. Rom. 1.18-20). It was almost universally agreed that the gods existed - even Epicureans admitted that - but it was almost as universally thought that the myths misrepresented the gods. By the second century CE, most Greek and Roman intellectuals either rejected the myths outright (the Epicurean approach), allegorized them into philosophical respectability (the Stoic approach), or claimed that the traditional gods were not gods at all, but mischievous daimones - spirits of the air - sent by the actual gods (the Platonic approach). This last interpretation became increasingly popular in Late Antiquity, when Neoplatonism emerged as the dominant philosophical tradition. By the time Constantine became Christian, very few educated Romans took their myths literally.

Christianity merely added another layer of allegory to the traditional pagan approaches to myth. Christian scholars resurrected the ancient allegorizing approach we call euhemerism (which claimed that the traditional gods were ancient human kings and heroes), and enthusiastically endorsed the idea that at least some myths were based on the deeds of demons masquerading as gods. The myths also offered conveniently low-hanging fruit for sermonizing; in the City of God, for example, Augustine describes Romulus' murder of Remus as characteristic of the sinful earthly city (15.5).

Whether Christian or pagan, however, every educated Roman continued to learn the myths, for the simple and sufficient reason that the myths were central to the literary canon on which their education was founded. The Aeneid was the supreme school text of late antiquity; papyri have even been found in Egypt with the poem's famous first line (arma virumque cano...) copied out over and over by schoolboys. Even committed Christians were assiduous readers of the classics; St. Jerome had a vision in his youth, in which a heavenly voice accused him of being "not a follower of Christ, but a follower of Cicero!"

The advent of Christianity, in short, did not fundamentally alter how the Romans viewed their foundation myths. As we have seen, most Romans already regarded these stories as, well, myths. Christianity simply confirmed this. Both before and after the Christianization of the Empire, likewise, the Romans regarded their foundation narratives as an integral part of their literary heritage. Romulus and Aeneas could be translated to allegory or assigned to devilry; but they could never be relegated to oblivion.

Thank you, both for this question and the answer. I love this group.