It's true that they were replaced, almost completely in northern Europe. But the claim of TFA is that these skeletons date from after this Indo-European / Yamnaya arrival, and hence that it disproves the theory that lactase persistence arrived with them.

Linguistically, I think we know they had cows but not agriculture, before migrating to Europe & India. (IIRC "cow" comes from PIE?) Which gave credence to the idea that they may have been lactose-tolerant. TFA is one study, so we will presumably eventually see whether this holds up with more data.