Lower Egypt, as archaeology has shown, was at a considerably lower level of civilization and technology than Upper Egypt, and was little more than a bunch of disorganized city states. Upper Egypt was the world's first relatively centralized state. Lower Egypt really had no chance to survive as a separate entity. If the Lower Egyptians somehow defeat and kill Narmer, Upper Egypt will be back to finish the job in the very near future under a different king. Basically the glories of the Old Kingdom of Egyptian civilization are delayed for a few years, nothing more.
Though I agree with most of this statement, I disagree with the inevitability of Upper Egypt's victory over Lower Egypt. Though at a lower level of technology, Lower Egypt did have certain things going for it.
-It had/has a greater area of arable land than Upper Egypt. More land = more agricultural produce = more people. Even today the Delta (Lower Egypt) supports the bulk of Egypt's population and is the nation's cultural hub. I don't think it's unreasonable to think that Lower Egypt sported a greater population than Upper Egypt in Narmer's day.
-Trade with the Mediterranean/Levant. Archaeology shows that later technological inventions (such as the advent of copper, and various pottery forms etc. IIRC) came through Lower Egypt.
Now, due to the severe paucity of actual historical evidence/records we are forced to speculate about the details of the "unification of Egypt". However, I think that had a figure managed to unite the populations of the Delta/Lower Egypt, this kingdom could very well have unified Egypt using it's ties with the Levant/Mediterranean world to defeat the relatively isolated Upper Egyptians during Egypt's formative years.
Now the ramifications of such an event are in many ways beyond our ability to fully comprehend due to the lack of historical source material. But here are some effects I can think of...
-Upper Egyptian Material Culture of OTL probably still dominates allo-Egypt due to it's previously mentioned superiority over Lower Egyptian pottery. However due to the political dominance of Lower Egypt I would expect to see more Semitic/Mediterranean influences over time.
-Egypt, especially the Old Kingdom, won't be as isolated as it was in OTL. This will have knock on effects in regards to religion and culture in addition to trade and geo-politics.
-Hieroglyphs might not develop in TTL as a less isolationist Egypt may adopt something similar to a Phoenician Script to facilitate trade.
-Without the guiding influences of Upper Egyptian Royal Culture the Pyramids may or may not make an appearance depending on how the dominant culture of Lower Egypt functions. If there are Pyramids in TTL they will undoubtedly be substantially different than OTL.
In Short an Egypt dominated by the Delta would be drastically different than our own Egypt and would change world history in numerous ways. Unfortunately due to our lack of knowledge about the details of the timeperiod we are limited to vague generalizations and unable to speculate further or with more accuracy.