The Vedanta Sutras, commentary by Sankaracharya (SBE34), tr. by George Thibaut  at sacred-texts.com
15. And on account of the atoms having colour, &c., the reverse (of the Vaiseshika tenet would take place); as thus it is observed.
Let us suppose, the Vaiseshikas say, all substances composed of parts to be disintegrated into their parts; a limit will finally be reached beyond which the process of disintegration cannot be continued. What constitutes that limit are the atoms, which are eternal (permanent), belong to four different classes, possess the qualities of colour, &c., and are the originating principles of this whole material world with its colour, form, and other qualities.
This fundamental assumption of the Vaiseshikas we declare to be groundless because from the circumstance of the atoms having colour and other qualities there would follow the contrary of atomic minuteness and permanency, i. e. it would follow that, compared to the ultimate cause, they are gross and non-permanent. For ordinary experience teaches that whatever things possess colour and other qualities are, compared to their cause, gross and non-permanent. A piece of cloth, for instance, is gross compared to the threads of which it consists, and non permanent; and the threads again are non-permanent and gross compared
to the filaments of which they are made up. Therefore the atoms also which the Vaiseshikas admit to have colour, &c. must have causes compared to which they are gross and non-permanent. Hence that reason also which Kanâda gives for the permanence of the atoms (IV, 1, 1, 'that which exists without having a cause is permanent') does not apply at all to the atoms because, as we have shown just now, the atoms are to be considered as having a cause.--The second reason also which Kanâda brings forward for the permanency of the atoms, viz. in IV, 1, 4, 'the special negation implied in the term non-eternal would not be possible 1' (if there did not exist something eternal, viz. the atoms), does not necessarily prove the permanency of the atoms; for supposing that there exists not any permanent thing, the formation of a negative compound such as 'non-eternal' is impossible. Nor does the existence of the word 'non-permanent' absolutely presuppose the permanency of atoms; for there exists (as we Vedântins maintain) another permanent ultimate Cause, viz. Brahman. Nor can the existence of anything be established merely on the ground of a word commonly being used in that sense, since there is room for common use only if word and matter are well-established by some other means of right knowledge.--The third reason also given in the Vais. Sûtras (IV, 1, 5) for the permanency of the atoms ('and Nescience') is unavailing. For if we explain that Sûtra to mean 'the non-perception of those actually existing causes whose effects are seen is Nescience,' it would follow that the binary atomic compounds also are permanent 2. And if we tried to escape from that difficulty by including (in the explanation of the Sûtra as given above) the qualification 'there being absence of (originating) substances,'
then nothing else but the absence of a cause would furnish the reason for the permanency of the atoms, and as that reason had already been mentioned before (in IV, 1, 1) the Sûtra IV, 1, 5 would be a useless restatement.--Well, then (the Vaiseshika might say), let us understand by 'Nescience' (in the Sûtra) the impossibility of conceiving a third reason of the destruction (of effects), in addition to the division of the causal substance into its parts, and the destruction of the causal substance; which impossibility involves the permanency of the atoms 1.--There is no necessity, we reply, for assuming that a thing when perishing must perish on account of either of those two reasons. That assumption would indeed have to be made if it were generally admitted that a new substance is produced only by the conjunction of several causal substances. But if it is admitted that a causal substance may originate a new substance by passing over into a qualified state after having previously existed free from qualifications, in its pure generality, it follows that the effected substance may be destroyed by its solidity being dissolved, just as the hardness of ghee is dissolved by the action of fire 2.--Thus there would result, from the circumstance of the atoms having colour, &c., the opposite of what the Vaiseshikas mean. For this reason also the atomic doctrine cannot be maintained.
392:1 Our Vaiseshika-sûtras read 'pratishedhabhâvah;' but as all MSS. of Sankara have 'pratishedhâbhâvah' I have kept the latter reading and translated according to Ânandagiri's explanation: Kâryam anityam iti kârye viseshato nityatvanishedho na syâd yadi kârane#py anityatvam ato#nûnâm kâranânâm nityateti sûtrârthah.
392:2 Because they also are not perceptible; the ternary aggregates, the so-called trasarenus, constituting the minima perceptibilia.
393:1 As they have no cause which could either be disintegrated or destroyed.
393:2 This according to the Vedânta view. If atoms existed they might have originated from avidyâ by a mere parinâma and might again be dissolved into avidyâ, without either disintegration or destruction of their cause taking place.