WARNING: This post contains nothing but SPOILERS.
Please read ALL Laird Barron stories before reporting back here.

The discussion includes flutes, pipes, panpipes, reeds, recorders, woodwinds, and whistles.

Flutes are (typically) cylindrical instruments which produce sound from the flow of air across an opening. The first flutes were naturally occurring caves, cavities, and reeds; wind was the first flautist. The vibrations created by the flow of air at the opening resonates within the body of the flute, and so varying the length of
the flute varies the sound produced. Introducing holes, which can be blocked with fingers as needed, effectively changes the length of the flute, allowing a single instrument to produce a range of sounds. Varying the air pressure will also vary the pitch produced by the flute.

Flutes are the earliest musical instruments produced by homo sapiens, if we ignore vocal sounds and percussive instruments. 35,000-year old [NY Times] and 45-000-year old bone [UKOM] flutes have been found. Due to their antiquity, flutes and percussion have come to be associated with "atavistic feelings", tapping into a "very old (and very powerful) region of our collective consciousness." [Classical.net] 

Long-associated with the Greek god Pan (“panic”, a sudden irrational fear without visible cause, is derived from Pan, since his voice would cause flocks to stampede), flutes in weird fiction seem to serve three main functions: have come to be associated with paganism, virility, (wild) nature, rituals, and (debauched) celebrations.

In weird fiction, piping seems to frequently serve one or more of the following functions:

a)      a signifier for an ancient/forgotten/forbidden/pagan ritual;
b)      a signifier for virility/debauchery/degeneracy/foreignness/alienness;
c)      a source of uncertainty/incongruity/strangeness.

The first two functions are difficult to disentangle – the ancient/forgotten/forbidden/pagan rituals are typically sources of horror, distasteful for the reasons listed in b.

The last function needs more explanation than the others. Flutes produce sounds which can be mistaken for sounds produced by the human vocal apparatus (especially in distressing situations), by birds, or by wind, given the right circumstances. Hearing piping , especially shrill, strident, or discordant  flutes, when one is not expecting
them, one can naturally question whether the sound was in fact produced by a musical instrument. This is not necessarily true of pianos, or guitars, for example.

Jethro Tull and primary school recitals aside, flutes are not commonly heard in the Western cultural milieu. Their presence signals something unusual. In the context of weird fiction, unusual is often synonymous with unpleasant and unwelcome.

Lovecraft memorably and consistently used flutes when describing the idiot court of the mindless outer god Azathoth.

What kept him from going with her and Brown Jenkin and the other to the throne of Chaos where the thin flutes pipe mindlessly was the fact that he had seen the name “Azathoth” in the Necronomicon, and knew it stood for a primal evil too horrible for description. (“The Dreams in the Witch House”)

And through this revolting graveyard of the universe the muffled, maddening beating of drums, and thin, monotonous whine of blasphemous flutes from inconceivable, unlighted chambers beyond Time; the detestable pounding and piping whereunto dance slowly, awkwardly, and absurdly the gigantic, tenebrous ultimate gods—the blind, voiceless, mindless gargoyles whose soul is Nyarlathotep. (“Nyarlathotep”)

It was the eldritch scurrying of those fiend-born rats, always questing for new horrors, and determined to lead me on even unto those grinning caverns of earth’s centre where Nyarlathotep, the mad faceless god, howls blindly to the piping of two amorphous idiot flute-players. (“The Rats in the Walls”)

that last amorphous blight of nethermost confusion which blasphemes and bubbles at the centre of all infinity—the boundless daemon-sultan Azathoth, whose name no lips dare speak aloud, and who gnaws hungrily in inconceivable, unlighted chambers beyond time amidst the muffled, maddening beating of vile drums and the thin, monotonous whine of accursed flutes; to which detestable pounding and piping dance slowly, awkwardly, and absurdly the gigantic ultimate gods, the blind, voiceless, tenebrous, mindless Other Gods whose soul and messenger is the crawling chaos Nyarlathotep. (“The Dream-Quest of Unknown Kadath”)

He thought of the ancient legends of Ultimate Chaos, at whose centre sprawls the blind idiot god Azathoth, Lord of All Things, encircled by his flopping horde of mindless and amorphous dancers, and lulled by the thin monotonous piping of a daemoniac flute held in nameless paws. (“The Haunter of the Dark”)

Azathoth aside, flutes and piping are also used to signal unhappy happenings:

I saw this, and I saw something amorphously squatted far away from the light, piping noisomely on a flute; and as the thing piped I thought I heard noxious muffled flutterings in the foetid darkness where I could not see. (“The Festival”)

Half gliding, half floating in the air, the white-clad bog-wraiths were slowly retreating toward the still waters and the island ruin in fantastic formations suggesting some ancient and solemn ceremonial dance. Their waving translucent arms, guided by the detestable piping of those unseen flutes, beckoned in uncanny rhythm to a throng of
lurching labourers who followed dog-like with blind, brainless, floundering steps as if dragged by a clumsy but resistless daemon-will. (“The Moon Bog”)

“O friend and companion of night, thou who rejoicest in the baying of dogs (here a hideous howl burst forth) and spilt blood (here nameless sounds vied with morbid shriekings), who wanderest in the midst of shades among the tombs (here a whistling sigh occurred), who longest for blood and bringest terror to mortals (short, sharp cries from myriad throats), Gorgo (repeated as response), Mormo (repeated with ecstasy), thousand-faced moon (sighs and flute notes), look favourably on our sacrifices!” (“The Horror at Red Hook”)

We find examples of piping used to create ambiguity and uncertainty in Lovecraft as well.

In “The Shadow Out of Time”, where the Elder Things in the basalt towers are associated with singular whistling noises (allowing that whistles are simple flutes):

thought of those possible five-circle prints and of what my dreams had  told me of such prints—and of strange winds and whistling noises associated with them. (“The Shadow Out of Time”)

The (cylindrical?) towers are also haunted by strong winds. Is the whistling indicative of alien monsters, or is it simply the result of the interaction between wind and towers? Why not both?

The din was my undoing. For, falsely or not, I thought I heard it answered in a terrible way from spaces far behind me. I thought I heard a shrill, whistling sound, like nothing else on earth, and beyond any adequate verbal description. It may have been only my imagination. (“The Shadow Out of Time”)

Probably I shrieked aloud then. I have a dim picture of myself as flying through the hellish basalt vault of the Elder Things, and hearing that damnable alien sound piping up from the open, unguarded door of limitless nether blacknesses. There was a wind, too—not merely a cool, damp draught, but a violent, purposeful blast belching savagely and frigidly from that abominable gulf whence the obscene whistling came. (“The Shadow Out of Time”)

“At the Mountains of Madness” provides the most elaborate example, since “musical piping” is practically one of the main characters. It is used throughout the story to provide sources of uncertainty and foreboding.

When first confronted by the sight of the eponymous mountains, we hear the first instance of musical piping:

The last lap of the voyage was vivid and fancy-stirring, great barren peaks of mystery looming up constantly against the west as the low northern sun of noon or the still lower horizon-grazing southern sun of midnight poured its hazy reddish rays over the white snow, bluish ice and water lanes, and black bits of exposed granite slope. Through the desolate summits swept raging intermittent gusts of the terrible antarctic wind; whose cadences sometimes held vague suggestions of a wild and half-sentient musical piping, with notes extending over a wide range, and which for some subconscious mnemonic reason seemed to me disquieting and even dimly terrible. (“At the Mountains of Madness”)

When the anatomy of the Old Ones is described:

Vocal organs seemed present in connexion with the main respiratory system, but they presented anomalies beyond immediate solution. Articulate speech, in the sense of syllable-utterance, seemed barely conceivable; but musical piping notes covering a wide range were highly probable. (“At the Mountains of Madness”)

When flashing forward to the end of their journey:

In five days more the Arkham and Miskatonic, with all hands and equipment on board, were shaking clear of the thickening field ice and working up Ross Sea with the mocking mountains of Victoria Land looming westward against a troubled antarctic sky and twisting the wind’s wails into a wide-ranged musical piping which chilled my soul to the quick. (“At the Mountains of Madness”)

When exploring the mountain range:

Even the wind’s burden held a peculiar strain of conscious malignity; and for a second it seemed that the composite sound included a bizarre musical whistling or piping over a wide range as the blast swept in and out of the omnipresent and resonant cave-mouths. There was a cloudy note of reminiscent repulsion in this sound, as complex and unplaceable as any of the other dark impressions. (“At the Mountains of Madness”)

When exploring the ruined city:

The speculations worked on his imagination, too; for in one place—where a debris-littered alley turned a sharp corner—he insisted that he saw faint traces of ground markings which he did not like; whilst elsewhere he stopped to listen to a subtle imaginary sound from some undefined point—a muffled musical piping, he said, not unlike that of the wind in the mountain caves yet somehow disturbingly different. (“At the Mountains of Madness”)

When deciphering the surprisingly informative pictograms on the walls of the ruined city:

The newly bred shoggoths grew to enormous size and singular intelligence, and were represented as taking and executing orders with marvellous quickness. They seemed to converse with the Old Ones by mimicking their voices—a sort of musical piping over a wide range, if poor Lake’s dissection had indicated aright—and to work more from spoken commands than from hypnotic suggestions as in earlier times. (“At the Mountains of Madness”)

When (unwisely) exploring deep within the underground portion of the ruined city:

“Tekeli-li! Tekeli-li!” That, I may admit, is exactly what we thought we heard conveyed by that sudden sound behind the advancing white mist—that insidious musical piping over a singularly wide range. (“At the Mountains of Madness”)

When confronted with a shoggoth:

Still came that eldritch, mocking cry—“Tekeli-li! Tekeli-li!” And at last we remembered that the daemoniac shoggoths—given life, thought, and plastic organ patterns solely by the Old Ones, and having no language save that which the dot-groups expressed—had likewise no voice save the imitated accents of their bygone masters. (“At the Mountains of Madness”)

When fleeing from the city:

I tried to keep all my skill and self-possession about me, and stared at the sector of reddish farther sky betwixt the walls of the pass—resolutely refusing to pay attention to the puffs of mountain-top vapour, and wishing that I had wax-stopped ears like Ulysses’ men off the Sirens’ coast to keep that disturbing wind-piping from my consciousness. (“At the Mountains of Madness”)

All this to say that there is a precedent for the use of piping and fluting in weird fiction, for a variety of purposes. Where Laird references Lovecraft’s Azathoth, we should not be surprised to find flutes:

the quaking mass at the center of everything where a sonorous wheedling choir of strings and lutes, flutes and cymbals crashes and shrieks and echoes from the abyss, the foot of the throne of an idiot god. (Vastation)

Listen. Do you hear them? Do you hear the flutes, Mac? I heard and then I saw. I beheld the demon sultan decked in red stars. (X’s For Eyes)

Horns and flutes played in a discordant chorus, blatting and shrilling. (X’s For Eyes)

echoes of a terrible clamor drifted to them around a river bend—a guttural chorus of whoops rose and fell in discordant rhythm with shrill blatts of flutes (X’s For Eyes)

Mac traveled at improbable velocity through freezing nothingness. Wheedles of an idiot flute trailed his passage. (X’s For Eyes)

The idiot flute melody issued from their slack mouths. (X’s For Eyes)

Causality, you understand? Cannot violate the laws of physics. But the pipes . . . (X’s For Eyes)

Elsewhere in his stories, they perform the functions we expect, alerting the reader to unwholesome people, activities, and places.

the awful piping ceased mid-note (Procession of the Black Sloth)

played shrill, discordant tunes on various woodwinds, she being the flautist so reviled in certain quarters of the LRA. (Procession of the Black Sloth)

“ (…) I couldn't figure out who was playing the flute. A panpipe, actually; high, thin, discordant. It pierced my brain.” (The Imago Sequence)

Panpipes, clashing cymbals, strobes of meteoric rain. (The Imago Sequence)

the piping shrilled, died, shrilled. (The Imago Sequence)

A reed pipe wheedled an almost familiar tune— (The Imago Sequence)

The nanny goat rolled its head on the altar and its eyes flared red to a surge of panpipes, an offstage Gregorian liturgy, thunderous laughter. (Catch Hell)

Fucking and dancing to wild flute music. (--30--)

And for an instant, the lush, shrill wheedle of panpipes drifted through the wood. (Blackwood’s Baby)

discordant vibration rippled over the ground and passed through Luke Honey’s bones—a hideous clash of cymbals and shrieking reeds reverberated in his brain. (Blackwood’s Baby)

Meanwhile a huge man in a red-and-black-checkered coat and coonskin cap pranced, nimble as a Russian ballerina, and wheedled a strange tune on a flute of lacquered black ivory. This flautist was a hirsute, wiry fellow with a jagged visage hacked from a stone, truly more beast than man by his gesticulations and the manner he gyrated his crotch, thrusting to the beat, and likely the product of generations of inbreeding, yet he piped with an evil and sinuous grace that captured the admiration of me, my companions, the entire roomful of seedy and desperate characters. (Hand of Glory)

joined his fellows in the wicked chant, this accompanied by the blowing of reeds and clashing of cymbals (The Croning)

His dreams were torments, full of fire and demons and reed music. (The Croning)

He imagined debauched reeds and clashing cymbals, demonic masks bathed in bloody firelight, an axe… (The Croning)

Conrad awakened occasionally to flickering orange shadows upon the ceiling; sing-song chants, the strident melody of reed pipes, the rhythmic kathud of drums. (The Light is the Darkness)

In a recent story, a flute (sorry, a recorder) takes the centre stage:

Objects of power are always named. Strident Caller is a recorder, not a flute. My family has passed her down through generations. Hollowed from a child’s radius in the days of antiquity, she belongs to a set of nine. A recorder, lyre, didgeridoo, hichiriki, drum, whistle, sitar, violin, and a horn.” Deborah went to the center of the kitchen. She breathed notes through the recorder. Her black silk robe clung to her breasts and hips as she swayed to a harsh, discordant melody. Thunder served as her metronome. Her playing was terrible and compelling. (Strident Caller)

Craven didn’t enjoy the shrill fluting either. Or the rolling thunder. The cacophony set his teeth on edge. Deborah ceased playing mid-note. “Not all music soothes the savage breast.” (Strident Caller)

I expect that fluting and piping will continue to make appearances in Laird's stories, performing their shrill functions with glee.