If I recall, most sentient life in the galaxy was wiped out at the end, with the protodevlin war.
And there might still be some protoculture left. The chronology's last mention of them says "near annihilation of Protoculture". Once their interstellar network and central government collapsed, it would be a lot harder to track down all the outlying colonies. So there could be a few protoculture worlds off in the far side of the Milky Way.
Very likely, or at least likely some additional Protoculture influenced worlds. The Zolan's have already been found afterall. Come to think of it, the way the AFOS left, and the way the Ginga Kujira left weren't entirely dissimilar, perhaps both were pieces of a test to finding the remaining Protoculture? I still say Sara & Shin will pop up in the next Macross Project..
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Speculation here but coudn't Shin & Sara have gone to have meet the "nearly extinct Protoculture' race? Perhaps as representatives of our peaceful culture.