With respect to the question of killing lice and treifos, the issue is what the source of the halacha is. If the halacha is pure sevara, then a clarification of the metziyus should change the halacha. If the halacha is kabalah from Har Sinai then a clarification of the metziyus would not change a halacha, we would just need to find a new explanation for the halacha.
For example, if the reason we pasken it is mutar to kill lice on Shabbos is purely a sevara because of the presumed metziyus of ???? ??? ????, then now that we know the metziyus is incorrect, the halacha should switch and follow R’ Eliezer. If, however, the Chachomim were matir killing lice on Shabbos because they had a kabala m’Sinai that it was mutar and ???? ??? ???? was just their sevara to explain the halacha, then even now that we know that they are ??? ???? the halacha would remain the same.
Although in the case of lice it is unclear, if I remember correctly, there is a list of treifos that are a halacha l’Moshe m’Sinai and therefore certainly apply regardless of the metziyus. In addition, there is a halacha that if an animal is hurt in a way that it will not live for 12 months, then it is a treifah even if the injury is not on the list we received from Sinai. For this latter din, the current metziyus is what would be relevant.