I just saw this actually happen. I was playing Rus. I left Nor barely alive - one island with population 1 - and focused on taking down Gothi. Just before I conquered the last Gothi island, it emitted a flotilla aimed at that last Nor island. I conquered the Gothi island with the Gothi flotilla still in transit and was told I had wiped out the Gothi. Out of curiosity, I let the ship arrive and conquer the Nor island (I assume I could have forestalled it by conquering the Nor island myself and winning). I then conquered that now-Gothi island and was told, again, that Gothi had been wiped out (and got the Victory screen). Apparently it doesn't break anything, but it looks a bit odd.