It's very simple...
I declared war against Egypt, Ramesses. While at war with Egypt, the Zulus destroyed the Egyptian civilization.
... many, many turns later my best ally made a colony, which happened to be Egypt, Kublai Khan. For some reason I started "at war" with this colony, vassal of my ally, and thus turning my best ally against me
Shouldn't the attitude and peace/war state be reset in these cases? It's afterall a new civilization, not the old civilization resurected.
I declared war against Egypt, Ramesses. While at war with Egypt, the Zulus destroyed the Egyptian civilization.
... many, many turns later my best ally made a colony, which happened to be Egypt, Kublai Khan. For some reason I started "at war" with this colony, vassal of my ally, and thus turning my best ally against me

Shouldn't the attitude and peace/war state be reset in these cases? It's afterall a new civilization, not the old civilization resurected.