The verse 2 Peter 3:16 does not equate the NT scripture with the OT "holy scriptures".
Graphas 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, the "the rest of" (τὰς λοιπὰς γρ) could also mean "the Scriptures as well". 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.