It is pretty hard to imagine any particular set of conditions short of total planetary surface destruction that would make all extremophiles go extinct - and as

It is pretty hard to imagine any particular set of conditions short of total planetary surface destruction that would make all extremophiles go extinct - and as long there is enough of them, they will start spreading again. Any particular species, including humans that lives on Earth is unlikely to survive catastrophic changes - but life will come back and spread into the newly freed and opened niches, just as it did before multiple times.