It wasn't just thought to have become extinct.
It was extinct.
Koutarou had some with him in Clan's ship.
Fresh from Ancient Forthorth, from the time of the Blue Knight himself.
I don't remember if there were seeds as part of that, or if Effie did some genetic engineering using samples of the tea, or what, but the sample he left with her is why it's no longer extinct.
So drinking it is always something that causes some feels, as it were.