I am well aware that modern Egyptians are descended from Arab conquerors that came thousands of years later.

Whilst modern Egyptians by and large speak Arabic, and most are Islamic - this is not because of some sort of 'proto-colonialism' where the Arabic invaders supplanted the locals. Supplanting a huge majority population occurs very rarely in history, and normally requires huge disease outbreaks, famine and destruction of infrastructure.

In nearly all pre-modern invasions and conquests, like the Arabic conquest of Egypt, the Norman invasion of England or Visigothic invasions of Iberia - where the local population is in the vast majority - what occurs is not a local population being replaced or settled by new people, but the local population is instead influenced by the conquerors. They might learn their language or convert religions for instance. This process, in regards to the Muslim conquests, is called Arabization.

Egypt has been one of the most heavily populated areas on Earth for a long time. At the time of the Muslim conquest it had a population in the millions - the Arabic army that conquered Egypt would have ranged from 4000 to 15'000. Even if every able-bodied man in the Arabian peninsula moved to Egypt, which they didn't - and couldn't have - local Egyptians would still be a vast majority.

In fact, Arabization took centuries in Egypt. It took centuries for the majority of the population to be Arabic speakers, or Islamic. For a long time the majority of Egyptians under Muslim rule spoke Coptic, and were Coptic Christians. The Coptic language is a descendant of the Ancient Egyptian language. To this day, Egypt has a very large Coptic Christian minority. The dialects of Arabic spoken in Egypt also have large amounts of Coptic loanwords.

Modern day Egyptians are the descendants of Ancient Egyptians. Genetic studies support this.