The Vedanta Sutras of Badarayana, Commentary by Sankara (SBE38), tr. by George Thibaut  at sacred-texts.com
43. As in the case of the offerings, (Vâyu and Prâna. must be held apart). This has been explained (in the Pûrva Mîmâmsâ-sûtra).
The section of the Vâgasaneyaka which begins, 'Voice held, I shall speak' (Bri. Up. I. 5, 21). determines Prâna to be the best among the organs of the body, viz. speech and so on, and Vâyu to be the best among the Devas, viz. Agni and so on.--Similarly in the Khândogya, Vâyu is affirmed to be the general absorber of the Devas, 'Vâyu indeed is the absorber' (IV, 3, 1), while Prâna is said to be the general absorber of the organs of the body, 'Breath indeed is the absorber' (IV, 3, 3).--The doubt here arises whether Vâyu and Prâna are to be conceived as separate or not.
As non-separate, the pûrvapakshin maintains; because in
their true nature they do not differ. And as their true nature does not differ they must not be meditated upon separately. Another scriptural passage also declares that the organs of the body and the divinities are non-different in their true nature, 'Agni having become speech entered the mouth,' &c. (Ait. Âr. II, 4, 2, 4). Moreover, the passage Bri. Up. I, 5, 13, 'These are all alike, all endless,' declares that the powers of the Devas constitute the Self of the organs of the body. And various other passages also testify to the fundamental non-difference of the two. In some places we have even a direct identification of the two, 'What Prâna is, that is Vâyu.' And in the sloka concluding the Vâgasaneyaka-chapter to which the passage under discussion belongs, the text refers to prâna only ('He verily rises from the breath and sets in the breath'), and thus shows the breath to be one with the previously mentioned Vâyu. This conclusion is moreover confirmed by the fact that the observance enjoined in the end refers to prâna only, 'Therefore let a man perform one observance only, let him breathe up and let him breathe down' (Bri. Up. I, 5, 23). Similarly, the Khândogya-passage, IV, 3, 6, 'One god swallowed the four great ones,' intimates that there is one absorber only, and does not say that one god is the absorber of the one set of four, and another the absorber of the other set of four.--From all this it follows that Vâyu and Prâna are to be conceived as one.
To this we make the following reply. Vâyu and Prâna are to be conceived separately, because the text teaches them in separation. The separate instruction given by the text with reference to the organs and the Devas for the purposes of meditation would be meaningless if the meditations were not held apart.--But the pûrvapakshin maintains that owing to the essential non-difference of Vâyu and Prâna the meditations are not to be separated!--Although, we reply, there may be non-difference of true nature, yet there may be difference of condition giving rise to difference of instruction, and, through the latter, to difference of meditation. And although the introduction of the concluding sloka. may be accounted for on the ground of its
showing the fundamental non-difference of the two, it yet has no power to sublate the previously declared difference of the objects of meditation. Moreover, the text institutes a comparison between Vâyu and Prâna, which again shows that the two are different, 'And as it was with the central breath among the breaths, so it was with Vâyu, the wind among those deities' (Bri. Up. I, 5, 22).--This explains also the mention made of the observance (I, 5, 23). The word 'only' (in 'Let a man perform one observance only') has the purpose of establishing the observance with regard to Prâna, by sublating the observances with regard to speech and so on, regarding which the text had remarked previously that they were disturbed by Death ('Death having become weariness took them'), and does not by any means aim at sublating the observance with regard to Vâyu; for the section beginning 'Next follows the consideration of the observances' distinctly asserts that the observances of Vâyu and Prâna were equally unbroken.--Moreover, the text, after having said, 'Let a man perform one observance only,' declares in the end that the fruit of that observance is the obtaining of (union with) Vâyu ('Then he obtains through it union and oneness with that deity'), and thus shows that the observance with regard to Vâyu is not to be considered as sublated. That by that 'deity' we have to understand Vâyu, we conclude from the circumstance that what the worshipper wishes to obtain is non-limitation of his Self 1, and that previously the term 'deity' had been applied to Vâyu, 'Vâyu is the deity that never sets.'--Analogously in the Khândogya-passage the text represents Vâyu and Prâna as different, 'These are the two absorbers, Vâyu among the Devas, Prâna among the prânas,' and in the concluding paragraph also (IV, 3,8) refers to them as distinct, 'These five and the other five make ten, and that is the Krita.'--For these reasons Vâyu and Prâna are to be conceived as different.
The Sûtra compares the case under discussion to a
parallel one from the karmakânda, by means of the clause, 'as in the case of the offerings.' With regard to the ishti comprising three sacrificial cakes, which is enjoined in the passage, Taitt. Samh. II, 3, 6, 'A purodâsa on eleven potsherds to Indra the ruler, to Indra the over-ruler, to Indra the self-ruler,' it might be supposed that the three cakes are to be offered together because they are offered to one and the same Indra, and because the concluding sentence says, 'conveying to all (gods) he cuts off to preclude purposelessness.' But as the attributes (viz. 'ruler' and so on) differ, and as scripture enjoins that the yâgyâ and anuvâkyâmantras are to exchange places with regard to the different cakes 1, the divinity is each time a different one according to the address, and from this it follows that the three offerings also are separate.--Thus, in the case under discussion, Vâyu and Prâna, although fundamentally non-different, are to be held apart as objects of meditation, and we have therefore to do with two separate meditations.--This is explained in the Saṅkarsha-kânda, 'The divinities are separate on account of their being cognized thus.'
But while in the case of the three purodâsas the difference of material and divinity involves a difference on the part of the oblations, we have in the case under discussion to do with one vidyâ only; for that the text enjoins one vidyâ only we conclude from the introductory and concluding statements. There is contained, however, in this one vidyâ a double meditative activity with regard to the bodily organs and the divinities, just as the agnihotra which is offered in the morning as well as in the evening requires a double activity. In this sense the Sûtra says, 'as in the case of the offerings.'
258:1 Agnyâdîn apekshyânavakkhino devo vâyus te tu tenaivâvakkhinnâ iti samvargaguno vâyur anavakkhinnâ devatâ. Ân. Gi.
239:1 The yâgyâ-mantra of the first offering being used as anuvâkyâ in the second one and so on.