Beware of taking these sort of statements too literally. As some have pointed out the “l’asid lavo” is discussing techiyas hameisim not the days of Moshiach.
After Moshiach comes the Sanhedrin HaGadol will reconvene and will have the power to reverse the ruling of any previous Sanhedrin HaGadol, including the ruling that we pasken like Bais Hillel over Bais Shammai. Whether or not the coming Sanhedrin will in fact rule like Bais Shammai will depend on the shikul hadas of the members of that Sanhedrin. There is no way to know whether or not any particular psak will change.