The verse 2 Peter 3:16 does not equate the NT scripture with the OT "holy scriptures". Only the latter believers started calling the NT as holy scripture. Two possibilities can be argued in favour of this view.
Firstly, Graphe does not necessarily mean "holy scripture" or "scriptures of the prophets" (Rom 1:2, 16:26, 2Ti 3:16, Mat 26:56), but scripture or writing in general. Peter's reference in the verse could simply be referring to the writings provided by the Apostles, or simply all writings pertaining to religion, that includes commentaries on the OT as well. Secondly, and this is the stronger argument: the "the rest of" (τὰς λοιπὰς γρ) should be translated as "the Scriptures as well" or "the Scriptures on the other hand" as demonstrated by Charles Bigg in 1901. See commentaries:
Ellicott comments,
The other scriptures.—The Old Testament cannot well be meant. St. Peter would scarcely have placed the writings of a contemporary side by side with the Scriptures of the Old Testament (the canon of which had long since been closed) without some intimation of a grouping which at that time must have been novel, and probably was quite unknown. It is much more probable that Christian writings of some kind are intended, but we can only conjecture which, any of the canonical writings of the New Testament then in existence, and perhaps some that are not canonical.
Cambridge Greek commentary:
ὡς καὶ τὰς λοιπὰς γραφάς. If the phrase occurred in a later document, we should not hesitate to render it “the rest of the Scriptures” and to take it as including both O.T. and N.T. Scriptures. But the fact that we have here a writing under the name of an Apostle, and of early date, causes a difficulty. We shall be overstating the case if we say that the writer here places Paul’s Epistles exactly on a level with the O.T. and implies the existence of a body of Christian Scriptures that were so regarded: but it is fair to say that he knows of the Pauline Epistles as writings read to Christian congregations and on the way to be put upon the level of Canonical Scripture.
Expositor's Greek Testament commentary,
(1) There has been much discussion among commentators as to the meaning of γραφάς
(graphas). Spitta takes γραφάς in sense of “writings,” and concludes that these were by companions of the Apostle Paul; but this is a very unusual sense of γραφή.... (2) The difficulty in connexion with the meaning of γραφάς is largely occasioned by the phrase τὰς λοιπὰς γρ. Does this mean that the Epistles of St. Paul are regarded as Scripture? Attempts have been made (e.g., by Dr. Bigg) to cite classical and other parallels that would justify the sense for τὰς λοιπὰς, “the Scriptures as well”. In these, certain idiomatic uses of ἄλλος and other words are referred to, but no real parallel to this sense of λοιπός can be found, and the connexion implied in λοιπός is closer than ἄλλος. The result of the whole discussion is practically to compel us to take τὰς λοιπὰς γραφάς in the obvious sense “the rest of the Scriptures,” and we cannot escape the conclusion that the Epistles of Paul are classed with these. The intention of the author of 2 Peter seems to be to regard the Pauline Epistles, or those of them that he knew, as γραφαὶ because they were read in the churches along with the lessons from the O.T.
- Here is the quote from Charles Bigg - A Critical And Exegetical Commentary On The Epistles Of St. Peter And St. Jude, p. 301-302 (1987 edition) (Google preview not available).
BDAG defines loipos as "Pertaining to being one not previously cited or included, other, rest of". The sense of remaining expressed by this word is that of the action has not been taken on this remainder group. This difference of being leftover is the kind of the contrast, it conveys.
Dr. Bigg used only two examples to show loipos means a contrasted-other; something contrasted or newly introduced in context. "But we do not want you to be uninformed, brothers, about those who are asleep, that you may not grieve as others do who have no hope". [1Th 4:13] and τὰ λοιπὰ ἔθνη (the other nations) from Deut 8:20 LXX, which is a common phrase. What others would not have noticed that loipos always means the contrasted rest of group which do not belong in the present category. There is no English equivalent that distinguishes a "contrasted other" like loipos (I am curious to know if other languages do have). The words like 'other, another, rest, remainder' in English means basically the same thing.
The commentators like "Expositor's Greek Testament" are wrong in claiming "but no real parallel to this sense of λοιπός can be found, and the connexion implied in λοιπός is closer than ἄλλος". The connexion with λοιπός is of a changed category, unlike the homogenous type as in ἄλλος. Compare some NT references for loipos.
'God, I thank you that I am not like other men, extortioners, unjust, adulterers, or even like this tax collector. [Luk 18:11 ESV] the rest who are unlike myself.
Do we not have the right to take along a believing wife, as do the other apostles and the brothers of the Lord and Cephas? [1Co 9:5 ESV] as opposed to the other apostles, who are unlike myself.
But we do not want you to be uninformed, brothers, about those who are asleep, that you may not grieve as others do who have no hope. [1Th 4:13 ESV]
So then let us not sleep, as others do, but let us keep awake and be sober. [1Th 5:6 ESV] a contrasted new-group of others
As for those who persist in sin, rebuke them in the presence of all, so that the rest may stand in fear. [1Ti 5:20 ESV] others who don't sin may fear
The rest of the dead did not come to life until the thousand years were ended. This is the first resurrection. [Rev 20:5 ESV]
For what is there in which you were made inferior to the rest of the churches [2 Cor 12:13] a change or contrast of class.
In contrast, allos αλλος means "other" of the same group or entity. Turn the other cheek; I say one servant go, and he goes, another 'come' and he comes; His hand was restored just the other; The other brother; Jesus presented another parable; Whoever marries another woman, etc. There is no contrast of "on the other hand" type, in these references.
The third Greek word is heteros, which means different, strange, of another kind; this another kind is already known or recoverable from the context, it simply means a different one. Ex. No one can serve two masters, he will love one, and hate the other; if they persecute you in one town, flee to another; are you the one or should we look for another one; Then it goes and brings with it seven other/different spirits more evil than itself; “Some say John the Baptist, different/others say Elijah, and different/others Jeremiah or one of the prophets.”
Conclusion:
Besides the argument given by various scholars about the timeline for the epistles, and the concept of a Canon in the Apostolic Church for objecting to the interpretation that Paul's letters are called scriptures, it should also be noted that for the apostles, to call their own writings as "scripture" would've been highly arrogant and inconceivable. The linguistic argument confirms that conclusion by showing that other languages like English do not have the same range of words in Greek, which led to the ambiguity and misinterpretation.
Had Peter used allos in stead of loipos in this verse, it would have meant that he is including the Scriptures in the same group as Paul's writings, showing a very close relationship between them. The word loipos on the other hand means, pertaining to be something of a new group. It means "Scriptures on the other hand, or as well". Given the fact that the English Bible versions & commentators fail to properly translate the scripture by learning basic Greek, we can safely accuse them of presenting inefficient ambiguity, and of even misleading the readers.