To be clear, I have ten potential flags here plus the fact that I have the two you suggested veebs, so don't consider them all to be used. In effect, don't use the term "leave out," we are here to do decide what we will use.
So basically from what I gather so far veBear is saying that I should avoid using Anubis altogether, and Xyth is suggesting that the lion is a good symbol for Nubia in general. So I think right now what I might do is use veBear's "Eagle" for the ancient and classical era, for medieval and renaissance I will use the second Makurian cross. For Industrial and modern I can use the Sudanese coat of arms/emblem.
Now, this is not what I'd like to use. Personally I'd like to use veBear's eagle as the ancient flag, one of the Anubis heads as their classical flag, the second Makurian cross for both the medieval and renaissance eras, and then the Sudanese emblem for the Industrial era. When there is a civ that doesn't actually exist in the modern era I like to use what-if flags, or at least aesthetically pleasing flags. In this case I would probably use a more stylized/modern looking Anubis flag. The logic behind this is that I can use more creativity since the Nubian nation didn't exist in a modern fashion, so I can kind of do what I'd like. To be honest I think the Anubis head looks really cool, so here is my suggestion in an easy-to-read form...
Ancient - veBear's Eagle hieroglyph
Classical - either veBear's Eagle hieroglyph or Anubis 1
Medieval - the second Makurian cross, it looks better
Renaissance - same as medieval, the second Makurian cross
Industrial - use the Sudanese coat of arms, or some variation of that
Modern - either use the Sudanese coat of arms again, or Anubis 4 or 5 since they look "modern"
Future - Anubis 4 or 5, simply because they have a modern/futuristic look
Thoughts?
EDIT: Now Xyth, the reason I am kinda leaning away from the lion's head, even though I think it is a very appropriate symbol for Nubia, is the simple fact that the lion can be used for many civilizations, including ones in the area. The Ethiopians use the lion of Judah and there would be two regional civs with that symbol. Not to mention the Hittites will be very lion-heavy and I don't want to "overdo" it with too many civs in one module pack. So while I agree with your assertion that it would be a great symbol, I think it could be better used in other areas.
EDIT 2: And yeah, I am wordy and overthink things, but this is what makes The Capo a great modder.