You lost nothing by sticking with vanilla D2. The two games were seperate. Even when you owned the expansion, you chose whether to make that character a vanilla character or an expansion character. All that said, the expansion was better, so there was little purpose to play vanilla if you owned it, but the option was still there.
Right now it's speculation based on the PTR and what little Blizz has released about what will change in vanilla once RoS hits.