There is a very good book for this, Roger Bagnall's Egypt in the Byzantine World. This should be your starting point.

It would most definitely not look like ancient Pharaonic Egypt, although many of the bigger monuments would still be around.

I personally would hazard that the cities of Egypt at this time would look more late Roman than Byzantine, the distinction being that the 6th century was a bit of a boom time for Byzantine Syria (not Anatolia though), and so a lot of the new construction would've paid more attention to contemporary architecture, i.e. more Byzantine (think the dead cities of Syria like Serjilla, but maybe the Byzantine/Late Roman distinction is a lot less than one would think). Egypt on the other hand would have continuous occupation and urban density from the ancient period, and thus would be in a position to continually refurbish existing buildings that still had use or build in a rather adhoc style not conducive toward a distinctive monumentalism if they weren't churches.

I say "hazard" a guess because my understanding is that residential archaeology inside the Egyptian urban centers is problematic because of continuous inhabitation straight up into our modern day. The reason why ruins are so great for archaeology is that they "fix" the building sites at a moment in time. If everyone is still living on top and rebuilding, there's only so much one can examine.

Not to mention that the people of the time would not be dressed like ancient Egyptians. All you have to do is look at any of the face paintings on late Roman Egyptian coffins to know that their hair and dress styles were clearly Roman at that period.

However, for reference points, I would say that you shouldn't think of these late Roman cities as similar to modern Egyptian cities. A lot of the changes in layout to the Roman cities taken over by the Arabs was due to (supposedly) the decline in importance of processions as legitimizing rituals and the increase of smaller scale merchants, thus the streets were narrowed to make room for more shops.

For that, Hendrik Dey's Afterlife of a Roman City would probably give more details.

In a nutshell, consider Byzantine Egypt thoroughly late Roman rather than "ancient Egyptian". Late Roman Antioch would probably be a good other city to relate it to (keeping in mind modern Antioch looks nothing like Roman Antioch).

Certainly an interesting question. Also quite a broad one, so answering it comprehensively isn’t going to be easy. I hope you excuse me if I’m not entirely up to the task. To begin I would say that plenty of things probably wouldn’t have looked all that different from Pharaonic Egypt. The basis for the Egyptian economy still was agriculture so the overwhelming majority of people were still living their lives as simple farmers very much like their ancestors thousands of years before. Also many of the pharaonic monuments must have been in a much better condition than they are today. Plenty of the temples had been still in use until quite recently after all. The emperors of the Early and High Imperial age had taken up the duty of the old pharaohs to maintain and enlarge many of those sanctuaries. Structures they newly build were continuing building traditions from older times. Take for example Trajan’s kiosk on the island of Philae in southern Egypt. Larger cities certainly had plenty of more hellenistic looking architecture as well, which used the Doric, Ionic and especially the Corinthian Order. Most of all this would have been the case for Alexandria, Egypt’s capital. It would still have housed most of its famous monuments like the Lighthouse of Pharos, which survived all the way into the middle ages.

On the other hand Late Antiquity was a time of great change for Egypt as it was elsewhere in the Mediterranean. At the beginning of the fourth century AD most of Egypt’s great sanctuaries seem already to have been closed. Why this was the case isn’t entirely clear. It might have had something to do with the spread of Christianity although this already happened before the conversion of Constantine the Great. The great sanctuary at Luxor is an interesting case. At the beginning of Late Antiquity it must have already been out of use because it was converted into a military camp at the end of the third century. This camp included a small sanctuary for the worship of the emperors of the first Tetrarchy which still keeps some of its painted decoration.

Some time after that the rise of Christianity to state religion became the death knell for the pagan cult sites. Again one example might suffice. In 391/2 AD a christian mob incited by Alexandria’s bishop Theophilos attacked the city’s most famous ancient sanctuary, the temple dedicated to the god Serapis. A decree by the emperor Theodosius I had ordered the end of all pagan cult practice only shortly before, which might have acted as an encouragement. The Christians plundered the compound, leveled its buildings and displayed the stolen objects for the whole city to see. A striking image from the fifth century Alexandrian World Chronicle shows bishop Theophilos triumphing on top of the cult statue of the defeated god. While certainly spectacular this episode isn’t necessarily representative of the majority of temple closures. Most probably happened much less violently and left the buildings intact as they were still seen as an adornment for their respective cities. So throughout Late Antiquity most Egyptian cities probably housed an array of former temples that over time were converted to some other use.

In the deep south of Egypt there was one pagan temple that remained an exception to this picture as it was kept in use even until the sixth century AD: the temple of Isis on the aforementioned island of Philae. This was part of an agreement the Romans had with the pagan tribes of neighboring Nubia which would still frequent this sanctuary. It was only closed down under the reign of Justinian I. By that time even the kingdoms of Nubia were being converted to Christianity.

With Christianity on the rise churches became the most prominent new buildings in Egypt’s cities as well as on the country side. There isn’t really enough space here to give anything like a comprehensive overview of early Coptic church architecture so I’m again leaving you with one example that shows how impressive those structures could get. The Red Monastery of Sohag in Upper Egypt was founded in the fourth century AD and received a new main church in the second halve of the fifth century. Like most Egyptian churches it was build as a basilica with three aisles. While its exterior was kept relatively plain the inside was richly decorated. At its eastern end the central nave gave way to sanctuary with three apses. The most striking feature of the Church and the reason I chose to focus on it are its wall paintings. Fortunately they have recently been renovated by the American Research Center in Egypt and can be viewed in all their glory here. I’ll leave you with this one example but you can always ask for more details about Coptic church architecture if you want to.

There is one example that gives a good insight into what a whole city in Late Antique Egypt would have looked like although it isn’t necessarily representative. I’m referring to Abu Mena near Alexandria, the holy city of Menas, one of Egypt’s foremost saints. Legend has it that the Holy Man’s relics were transported by two camels to find a burial place for him and when they reached the place where Abu Mena would later be located the animals refused to go any further. So Menas was buried there and later a whole city developed around his cult site. This legend is the reason why the saint is almost always depicted with two camels by his side. Abu Mena is quite an important archaeological site as it is one of the few cities that were newly founded in Late Antiquity. The fact that it wasn’t build over in later times further increases its importance. The city’s layout was dominated by the main processional road that led from the northern gate all the way down to the saint’s sanctuary. The street was lined by columned halls on both sides. Countless little shops were located inside of them. Similar streets would have been a feature of all of Egypt’s major cities. The city center looked like this. At the northern end of the plan you can see one of Abu Menas bathing houses. It shows that the antique practice of building large public baths hadn’t gone out of style yet. The buildings further south with the large rectangular courtyards are the xenodochia which housed the pilgrims that came to visit Menas. On its southern end the processional road leads into a huge open square from which the pilgrims could access two large churches, one of which build directly above Menas’ tomb, a baptistery a well as another courtyard where sick people could receive treatment. Its nature as a destination for huge crowds of pilgrims means that Abu Mena certainly wasn’t your typical Egyptian city. But I don’t know of any other place in Egypt where a late antique urban center can be studied this completely.

Literature: Roger S. Bagnall, Egypt in Late Antiquity (1995); Peter Grossmann, Abu Mina. A guide to the ancient pilgrimage center (1986); Michael Jones – Susanna McFadden, Art of Empire. The Roman Frescoes and Imperial Cult Chamber in Luxor Temple (2015).

I'm not sure how the rules work but can I take an opportunity to ask my own question?

I read on wikipedia that after the Greeks took over they created a segregated system where they were on the top and Native Egyptians were on the bottom. A system that Romans kept and placed themselves with the Greeks on top. Egyptians were servants and slaves and led such a miserable life they converted to Christianity but the divide still existed and they choose to have a different one (coptic) rather then what the Romans wanted.

The divide seems to have lasted from 300BC to 600 AD because when I studied Arabic history I found out that Greek speakers fled the Arab conquest while the majority of Egyptians didn't. They also barely lifted a finger to resist the tiny Arab force even though they didn't like them. Did the same also occur in Syria? The reason I ask is because the Arabs successfully ruled as a minority in the beginning by living separately from Syrians and Egyptians and even got their help to create a Navy. Something they who just came from Arabia didn't have the experience in building or running.

I find it odd that Egyptians would put up with this for centuries.