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In several places, the mishna describes how water and blood in the slaughterhouse in the Temple are "pure". In his commentary on the mishna Eduyot 8:4, the Bartenura describes a disagreement as to what this means:

משנה: הֵעִיד רַבִּי יוֹסֵי בֶּן יוֹעֶזֶר, אִישׁ צְרֵדָה, עַל אַיִל קַמְצָא, דָּכָן. וְעַל מַשְׁקֵה בֵית מִטְבְּחַיָּא, דְּאִינּוּן דַּכְיָן. וּדְיִקְרַב בְּמִיתָא, מִסְתָּאָב. וְקָרוּ לֵיהּ, יוֹסֵי שָׁרְיָא:

רע״ב ד״ה דאינון דכיין. איכא מאן דאמר דכיין טהורים לגמרי. דטומאת משקין לאו דאורייתא אלא רבנן הוא דגזור בהו טומאה, ובהני לא גזור. ואיכא למ״ד דכיין טהורים מלטמא אחרים, אבל טומאת עצמן יש להן, דיש למשקין טומאה מן התורה להטמא ולא מצו רבנן לטהר מה שטמאה התורה:

Mishna: Rabbi Yose ben Yoezer, a man of Zereda, testified concerning the ayal-locust, that it is pure; And concerning liquid in the slaughter-house (of the Temple), that it is pure; And that one who touches a corpse is impure. And they called him "Yose the permitter".

Bartenura s.v. d'inun dakhyan: There are those who say that "pure" means compeltely pure, as the tumah of liquids isn't Biblical, but rather the Rabbis decreed tumah on them, and on these [the liquids in the slaughterhouse] they didn't decree [tumah]. And there are those who say that "pure" means they do not make other things impure, but they themselves are susceptible to tumah, because liquids are susceptible to tumah Biblically, and the Rabbis cannot declare pure what the Torah declares impure.

This disagreement is described in Bavli Pesachim 16a and onward.

In his commentary to Keilim 15:6, the Bartenura writes differently:

משנה: נִבְלֵי הַשָּׁרָה, טְמֵאִין. וְנִבְלֵי בְנֵי לֵוִי, טְהוֹרִין. כָּל הַמַּשְׁקִין, טְמֵאִין. וּמַשְׁקֵה בֵית מַטְבְּחַיָּא, טְהוֹרִין. כָּל הַסְּפָרִים מְטַמְּאִין אֶת הַיָּדַיִם, חוּץ מִסֵּפֶר הָעֲזָרָה. הַמַּרְכּוֹף, טָהוֹר. הַבַּטְנוֹן, וְהַנִּקְטְמוֹן, וְהָאֵרוּס, הֲרֵי אֵלּוּ טְמֵאִים. רַבִּי יְהוּדָה אוֹמֵר, הָאֵרוּס טָמֵא מוֹשָׁב, מִפְּנֵי שֶׁהָאַלָּיִת יוֹשֶׁבֶת עָלָיו. מְצֻדַּת הַחֻלְדָּה, טְמֵאָה. וְשֶׁל הָעַכְבָּרִין, טְהוֹרָה:

רע״ב ד״ה טהורין(ב). שהם אינם מקבלין טומאה, ולא מכשירין האוכלים לקבל טומאה:

Mishna: Ordinary harps are susceptible to impurity, but the harps of Levites are clean. All liquids are susceptible to impurity, but the liquids in the Temple slaughtering house are clean. All scrolls convey impurity to the hands, excepting the scroll of the Temple courtyard. A wooden toy horse is clean. The belly-lute, the donkey-shaped musical instrument and the erus are susceptible to impurity. Rabbi Judah says: the erus is susceptible to sitting impurity since the wailing woman sits on it. A weasel-trap is susceptible to impurity, but a mouse- trap is clean.

Bartenura s.v. tehorim(2): As they [liquids in the slaughterhouse] are not susceptible to tumah, and do not "prepare" [מכשיר] foods to be susceptible to tumah.

In these comments, the Bartenura doesn't describe a disagreement, but only one side of it (that the tumah is Rabbinic), and also adds an additional fact (that the liquids don't "prepare" food to be susceptible to tumah) not mentioned in his comments on Eduyot.

What reason is there for the disparity in commentary? Do the latter comments mean that the Bartenura holds that the tumah of liquids is Rabbinic (while it seems to me that the discussion in Pesachim is left open)?

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