I logged in to a new world I started yesterday, where I had built a house out of dark oak planks, as well as birch and regular oak. Having logged in, "waking up" in the house, the dark oak planks had changed to regular oak, while the parts that were regular oak and birch were unchanged. The dark oak wood and planks in my inventory had disappeared, and also the entire dark oak forest a short distance from the house, except for one tree which I think was from a sapling I planted yesterday. The few other trees of other kinds were still there.

It seems it happened as I logged in today. I think just played one long session yesterday with out logging out once.