The problem of Professor X being alive isn’t resolved by the future timeline being erased. The contradiction is that he died in The Last Stand — but is alive in the future we see at the beginning of DOFP. THAT’S the Xavier who shouldn’t exist. It makes sense that everything has changed going forward from the END of the movie; it doesn’t make sense that Xavier would still exist in the original timeline after having died in X3. As they say in Doctor Who, “timey-wimey”!!