I cheked Irenaeus’ Against Heresies 3.16.5 and 3.16.8. It seems to me Irenaeus quoted 1 and 2 John but not from 3 John (English translation from Anti Nicene Fathers with added Scripture reference)

Therefore did the Lord also say to His disciples after the resurrection, “O thoughtless ones, and slow of heart to believe all that the prophets have spoken! Ought not Christ to have suffered these things, and to enter into His glory?” And again does He say to them: “These are the words which I spoke unto you while I was yet with you, that all things must be fulfilled which were written in the law of Moses, and in the prophets, and in the Psalms, concerning Me. Then opened He their understanding, that they should understand the Scriptures, and said unto them, Thus it is written, and thus it behoved Christ to suffer, and to rise again from the dead, and that repentance for the remission of sins be preached in His name among all nations.” Now this is He who was born of Mary; for He says: “The Son of man must suffer many things, and be rejected, and crucified, and on the third day rise again.” The Gospel, therefore, knew no other son of man but Him who was of Mary, who also suffered; and no Christ who flew away from Jesus before the passion; but Him who was born it knew as Jesus Christ the Son of God, and that this same suffered and rose again, as John, the disciple of the Lord, verifies, saying: “But these are written, that ye might believe that Jesus is the Christ, the Son of God, and that believing ye might have eternal life in His name,”—foreseeing these blasphemous systems which divide the Lord, as far as lies in their power, saying that He was formed of two different substances. For this reason also he has thus testified to us in his Epistle: “Little children, it is the last time; and as ye have heard that Antichrist doth come, now have many antichrists appeared; whereby we know that it is the last time. They went out from us, but they were not of us; for if they had been of us, they would have continued with us: but [they departed], that they might be made manifest that they are not of us. Know ye therefore, that every lie is from without, and is not of the truth. Who is a liar, but he that denieth that Jesus is the Christ? This is Antichrist.” (1 John 2:18-19, 21-22, loosely quoted)
Irenaeus, Against Heresies 3.16.5

All, therefore, are outside of the [Christian] dispensation, who, under pretext of knowledge, understand that Jesus was one, and Christ another, and the Only-begotten another, from whom again is the Word, and that the Saviour is another, whom these disciples of error allege to be a production of those who were made Æons in a state of degeneracy. Such men are to outward appearance sheep; for they appear to be like us, by what they say in public, repeating the same words as we do; but inwardly they are wolves. Their doctrine is homicidal, conjuring up, as it does, a number of gods, and simulating many Fathers, but lowering and dividing the Son of God in many ways. These are they against whom the Lord has cautioned us beforehand; and His disciple, in his Epistle already mentioned, commands us to avoid them, when he says: “For many deceivers are entered into the world, who confess not that Jesus Christ is come in the flesh. This is a deceiver and an antichrist. Take heed to them, that ye lose not what ye have wrought.” (2 John 7-8) And again does he say in the Epistle: “Many false prophets are gone out into the world. Hereby know ye the Spirit of God: Every spirit that confesseth that Jesus Christ is come in the flesh is of God; and every spirit which separates Jesus Christ is not of God, but is of antichrist.” (1 John 4:1-3) These words agree with what was said in the Gospel, that “the Word was made flesh, and dwelt among us.” Wherefore he again exclaims in his Epistle, “Every one that believeth that Jesus is the Christ, has been born of God;”(1 John 5:1) knowing Jesus Christ to be one and the same, to whom the gates of heaven were opened, because of His taking upon Him flesh: who shall also come in the same flesh in which He suffered, revealing the glory of the Father.
Irenaeus, Against Heresies 3.16.8

With reference to the combining of Johannine epistles …
The church fathers did, at times, refer to more than one of the Johannine epistles as a single epistle. See, e.g., Irenaeus, Adversus Haereses, 3:16:5 and 3:16:8, where Irenaeus states that he’s quoting from a single epistle, even though the quotations come from two different Johannine letters. See also the work of Peter Katz, “The Johannine Epistles in the Muratorian Canon,” JTS 8 (1957): 273-74, for a slightly different angle.

As for Codex Claromontanus, it is fairly clear that Philippians and the Thessalonian epistles were dropped out in copying the stichometric list. As for Hebrews … I must admit that I am in error at that point; in typing that list, I fell victim to parablepsis! More than a dozen academic reviewers of the manuscript, from many faith backgrounds, and none of them caught that! Thanks for noticing; I will see if that can be corrected in the next edition.

When I stated that Athanasius was representing a previously-extant canonical standard, my intended meaning was that his list was based on a previous canonical standard of eyewitness testimony, though perhaps that could have been more clearly stated in the text.