John Smith, 'boling', and the 'boling knot'
The term Boling knot appears in John Smith, A Sea Grammar: With the Plaine Exposition of Smiths Accidence for young Sea-men, enlarged, published not in 1691 (as the Wikipedia article on bowline erroneously states) but in 1627. Here is the relevant paragraph from Smith's Grammar:
Now to make an end of this discourse with a knot, you are to know, Sea-men use three, the first is called the Wall knot, which is a round knob, so made with the strouds or layes of a rope, it cannot slip; the Sheates, Takes, and Stoppers use this knot. The Boling knot is also so firmely made and fastened by the bridles knot. into the creengles of the sailes, they will breake, or the saile split before it will slip. The last is the Shepshanke, which is a knot they cast upon a Runner or Tackle when it is too long to take in the goods, and by this knot they can shorten a rope without cutting it, as much as they list, and presently undoe it againe, and yet never the worse.
Elsewhere in the same chapter of the Grammar (titled "How all the Tackling and Rigging of a Ship is made fast one to another, with their names, and the reasons of their use"), Smith discusses the function of the boling itself:
The Boling is made fast to the leech of the saile about the middest to make it stand the sharper or closer by a wind, it is fastened by two, three, or foure ropes like a crows foot to as many parts of the saile which is called the Boling bridles, onely the missen Boling is fastened to the lower end of the yard, this rope belongs to all sailes except the Spret-saile, and Spret-saile Top-saile, which not having any place to hale it forward by, they cannot use those sailes by a wind : sharp the maine Boling is to hall it taught : hale up the Boling is to pull it harder forward on : checke or ease the Boling is to let it be more slacke.
This John Smith is most familiar to people today as the Englishman in the Pocahontas story. Smith uses the word line in the sense of "rope" multiple times in the course of the Grammar, and he identifies certain specific types of rigging in compounds that use that spelling: leech lines, Knave- line, smiting line, clew line, rayling lines, Dipsie line, Log line, Sounding line. The three exceptions to this usual pattern are boling, ratling ("all those small ropes doe crosse the Shrouds like steps are called Ratlings"), and marling ("Marling is a small line of untwisted hemp, very pliant and well tarred, to sease the ends of ropes raveling out, or on the sides of the blockes at their arses").
As for bow, Smith spells that word in his Grammar as you'd expect him to when it stands alone, as in the chapter on ship building:
It were not amisse now to remember the Fore-castle, being as usefull a place as the rest, this is the forepart of the Ship above the Decks over the Bow ; there is a broad Bow & a narrow Bow, so called according to the broadnes or the thinnesse : the Bow is the broadest part of the Ship before, compassing the Stem to the Loufe, which reacheth so farre a the Bulk-head of the Fore-castle extendeth. Against the Bow is the first breach of the Sea, if the Bow be too broad, she will seldome carry a fome before her : where a well bowed Ship so swiftly presseth the water, as that it foameth, and in the darke night sparkleth like fire. If the Bow be too narrow, as before is said, she pitcheth her head into the Sea, so that the meane is the best if her after way be answerable.
Of course, this spelling provides no clear indication as to whether the normal pronunciation of bow in Smith's time rhymed with "how" or with "low."
If a bowline is (as Merriam-Webster's Eleventh Collegiate Dictionary reports) "a rope used to keep the weather edge of a square sail taut forward"—that is, toward the bow—there is little reason for Smith to have preferred the spelling boling over bow line unless (in 1627) "boling" closely approximated the standard sea-man's pronunciation of the term at that time. This in turn would suggest that the pronunciation 'bō-lən (to use Merriam-Webster's system of pronunciation symbols), which the Eleventh Collegiate gives as the more common pronunciation of bowline today ('bō-'līn is the only other named variant) was already very nearly in place in English speech in 1627.
Other early matches for 'boling', 'bow-line', and 'bowline'
Boling also appears (and bowline does not) in Elisha Coles, An English Dictionary: Explaining the Difficult Terms that are used in Divinity, Husbandry, Physick, Philosophy, Law, Navigation, Mathematicks, and Other Arts and Sciences (1676):
Boling, the Cord that draws the sail to gather wind.
This same entry, with minor changes in capitalization, also appears in editions of Coles as late as 1732.
Nathaniel Bailey, Dictionarium Britannicum: Or a More Compleat Universal Etymological English Dictionary (1730), however, lists two spellings—bow-line and bowling:
BOW-LINE, BOWLING {with Mariners} a rope made fast to the leetch of the outside of a sail, by 2, 3, or 4 other ropes, like a crow's foot, which is called the Bowling bridle. Its use is to make the sails stand sharp or close by a wind.
BOWLING Knot {with Sailors} a sort of knot that will not slip, by which the bowling bridle is fastened to the crengles.
However, Bailey's An Universal Etymological English Dictionary, second edition (1731) drops the entries for bowline/bowling and for bowling knot, and retains only a brief three-part entry for check the bowline, ease the bowline, and run up the bowline, defined as "{Sea terms} which import, let it be more slack."
The earliest match for the spelling "bowline knot" is from Daniel Baron Lescallier, Vocabulaire des termes de marine anglois et françois (1777), a French-English dictionary of nautical terms:
Bowline-knot, Nœud de bouline.
But an English-Swedish dictionary from 20 years early has no compunction about switching from bowline to boling-knot in the same block of phrase translations. From Jacob Serenius, An English and Swedish Dictionary (1757):
BOWLINE, bog-lina. Hale up the bowline, holl an bog-linan, hala up bog-linan. Ease the Bowline, fyr på bog-linan. Sharp the Bowline, drag hårdare til bog-linan. Bowling-knot, en hård knut, som icke går up igen eller losnar.
Even earlier, Daniel Defoe, in Letter 53 of Miscellany Letters: Selected out of Mist's Weekly Journal (1722) opens one with the salutation "Mist, you Haul-Bowline Dog..."
William Falconer, An Universal Dictionary of the Marine (1784) has multiple instances of bowline, including this entry for the term:
BOWLINE (boulin, Fr.) a rope fastened near the middle of the leech, or perpendicular edge of the square sails, by three or four subordinate parts called bridles. It is only used when the wind is so unfavourable that the sails must all be braced sideways, or close-hauled to the wind : in this situation the bowlines are employed to keep the weather, or windward, edges of the principal sails tight forward and steady, without which they would be always shivering, and rendered incapable of service.
Best Answer
I don't know of any word where "pph" has been replaced with "ph". The fact that we only have "sapphire" and "Sappho," both starting with "sa-" (and of course related words and names such as Sapphic/sapphic, Sapphira), seems to be a coincidence.
It seems this was a rare sequence of sounds in Greek, like the "tth" of "Matthew":
In Greek, the π is not silent. In modern Greek, the sequence "πφ" would be pronounced /pf/; you can hear this in JovannaK's pronunciation of Σαπφώ on Forvo. Ancient Greek is thought to have had aspirated consonants and doubled or long ("geminate") consonants in some contexts; the ancient pronunciation of "πφ" is, as Janus says, reconstructed as something like /p.pʰ/, distinct from "singleton" φ /pʰ/. (The pronunciation of peri22b on Forvo seems to be aimed towards this /p.pʰ/ realization.)
I'm not an expert, but my impression is that in Ancient Greek, aspiration contrasts were mostly neutralized for plosives that came before other obstruents. The neutralized sound could be written in various ways, some of which were probably conventional; e.g. when the second consonant was an aspirated plosive, the first seems to have also generally been written with a letter for an aspirated plosive (hence the common occurence in English words of Greek origin of sequences like "phth" and "chth"); when the second consonant was the fricative /s/, the special letters ψ and ξ were used, and so on. It seems that /p.pʰ/ and /t.tʰ/ were usually written as πφ and τθ respectively but the alternative spellings φφ and θθ were also possible in some eras (History of the Greek Alphabet, by Evangelinus Apostolides Sophocles, 1848); maybe they represented a difference in pronunciation as well or maybe not.
In Greek, generally the letters Φ ("ph"), θ ("th") and χ ("ch") were used to transcribe Hebrew ף ("p/f"), ת ("t/th"), and ך ("k/kh") respectively, or the corresponding sounds in a similar Semitic language such as Aramaic. (this is a simplification, but I can't give a more nuanced description because I'm not an expert)
(Side note about something that can cause a bit of confusion: Hebrew has rules assigning a fricative pronunciation to these some of these letters in certain contexts, and a plosive pronunciation in other contexts; the precise rules are a bit different and apply to different letters in different varieties of Hebrew. The Greek transliteration generally is not at all related to this phenomenon in Hebrew: the letters Φ θ χ may correspond to Hebrew plosives as well as Hebrew fricatives. The explanation I've seen for the Greek transcription system is that even the plosive allophones of the corresponding Hebrew consonants were aspirated, making them match better to Greek Φ θ χ than Greek π τ κ. Greek τ κ were the standard equivalents to Hebrew ט ("t", formerly contrastively "emphatic" compared to ת, and probably unaspirated) and ק ("q/k", formerly uvular or emphatic, and probably unaspirated). See the answer on Linguistics SE to Why was the name תאומא transliterated as Θωμᾶς (Thomas) rather than Τωμᾶς (Tomas)?)
The sequence "πφ" was used in Greek to represent geminate or double-length Hebrew/Aramaic ף, "pp". But there are not many words with this sound that were loaned from Hebrew/Semitic to Greek, and then brought into English. Sapphire is one: Wiktionary says
Another example, that is an obscure name, is "Jonathan Apphus" (Wikipedia says "Hebrew: יונתן הוופסי, Ancient Greek: Ἰωνάθαν Ἀπφοῦς"; "JONATHAN MACCABEUS" on Jewish Encyclopedia says "Syriac הפּוש" which looks a bit closer to "Ἀπφοῦς" going by the little I know of the Hebrew alphabet).
I have no idea where "Sappho" comes from, but as you say, "there appears to be no etymological link" so it seems extremely doubtful that the similarity to the start of "sapphire" is anything but a coincidence. (If anyone knows, please post the answer to the following Linguistics SE post: Two questions about Sappho's name.)
The modern English pronunciation can probably be explained by considerations within the sound system and orthographic system of English (the sound sequence /pf/ is awkward, and in many cases doubled letters are pronounced the same as single letters in English, so there's no strong pressure from the orthography to use /pf/ rather than /f/).