Correct. We do not and cannot unless gadol bechachma ubeminyan. That is the main idea of mesorah. That is why we have mishnah and gemara, to know how they paskened. A pair of tefillin found at masada does not qualify for that it it argues on the gemara.
One recent issue that has reversed this whole thing is worms in fish. The gemara and shulchan aruch say it’s muttar, and some are saying we rely on science over mesorah and say they are assur.
Another big issue is the 167-year discrepancy between secular dating and Rabbinic dating- 586 vs 422 bce. The question is, is going like secular dating violating a halacha or not.