Anemia may be an interesting indicator here, because it could imply several possibilities, both in its cause and effects.
The assumption that the anemia was caused by malnutrition, and associated with protein deficiency may be correct, or it could be hereditary, or even caused by a disease or huge swarms of blood sucking parasites. Or a combination of the above.
In turn, the idea that this was a new city, yet was abandoned after this one pharaoh, also implies some interesting things. Leaving a previously inhabited area needs a strong motivation.
Perhaps something bad befell the old city, and was so awful that it resulted in the traditional gods being temporarily abandoned as ineffectual.
The Exodus dates to around this time, which would give good reason to abandon the Gods of old.