Commentaire sur Le Deutéronome 27:2

והקמת לך THEN THOU SHALT RAISE THEE UP [GREAT STONES] — in the Jordan, and afterwards you shall take out from there others and build an altar of them on Mount Eval. Consequently you must say that there were three sets of stones: twelve in the Jordan, an equal number in Gilgal, and another twelve on Mount Ebal, as is stated in Treatise Sotah 35b.

ושדת אותם בשיד, “and you shall coat them with plaster.” The Torah did not use the term גיר, chalk, in this instance as the prophet Isaiah 27,9 used when describing shattered altar stones. This in spite of the fact that גיר is a far stronger material than שיד. The reason the Torah ordered the stones to be covered with שיד is that this is a material which stands up to rain better than גיר.

There were three kinds of stones, etc. Nothing can be proved from the verses here. Rather, everything is proved from the verses in Yehoshua. It is written there (4:2) that they erected twelve stones in the Jordan at the place where the kohanim's feet stood, and they erected twelve stones in Gilgal, the first place they sojourned in the Land of Israel. And on those stones [of Gilgal] Yehoshua had previously written the whole Torah at Mount Eival. Because sefer Yehoshua mentions these two types of stones, i.e. those of the Jordan and those of the Gilgal, Rashi therefore mentions them first, even though they [i.e. the ones of Gilgal] were first erected at Mount Eival. But because they removed them, and took and erected them in Gilgal, Rashi mentions them [those of the Jordan and the Gilgal] together. Regarding this Rashi writes “As stated in Tractate Sotah,” because that is where the verses of sefer Yehoshua are cited. And when Rashi writes “three kinds of stones,” he means [two kinds at] three different sites. This answers the questions raised by Re”m against Rashi from Tractate Sotah Chapter Eilu Ne'emarin.