Rapiqum 👉 Habban
Undiscovered Kassite settlement or city-state. Not known if it was closer to Babylon than Kazalla, but, it controls Kazalla and Kazalla was secondary or perhaps even abandoned at that point, so I am giving preference to Habban as the centre of this polity.

Ramesses (faction) 👉 Pa-Kanana
The easternmost Egyptian province, literally The Canaan. Like many Egyptian names, shared its name with the actual country Canaan, and with the city Pa-Kanana, the administrative centre of Egyptian Canaan in actual Egyptian territory (compare: Egyptian province Ta-seti and the actual non-Egyptian country Ta-seti right on the opposite side of the border). In the game, Ramesses does not control the city Pa-Kanana, so initially I thought it would be improper to name his faction this. However, his faction is effectively what Pa-Kanana was in real life, and he almost always conquers Pa-Kanana immediately after the game starts anyway, so I have reconsidered my approach and decided to tell a little story of an unrecorded uprising in Pa-Kanana, with the faction Sukkot representing local rebels.
Sheru 👉 Setjet
Common Egyptian name for the area.
Beersheba (faction) 👉 Mentju
People who lived in Setjet, according to Egyptian sources.
Kaftiu (province) 👉 Kaft
Kaftiu is the ethnonym for the people who live in Kaft the place.
Uiram 👉 Tukkama
Hayasha 👉 Aripsa
Uiram and Hayasa are tribal names rather than settlement names. We know Mursili II conquered a settlement called Aripsa on the shore of an unidentified body of water, and Tukkama shortly after, during his war against Hayasa. In the game, the settlement Hayasha is close to Lake Van, and Uiram is the second settlement that belongs to the playable Hayasa faction, making this re-assignment a no-brainer.
Nimrud 👉 Kalhu
Nimrud is a recent rename; Kalhu was still called Kalhu even in the early Iron Age.
Teisheba 👉 Teishebaini
The god Theispes is attested and the city-state Teishebaini named after him is attested but no Teisheba.
Kammanu 👉 Azzi
Kammanu is an Iron Age name that only comes about after the Hittite Kingdom falls. Azzi is how the area east of Isuwa was known.
Hayasa-Azzi 👉 Hayasa
Because I separated Hayasa and Azzi.
Melid 👉 Hinzuta
Melid is just a different spelling of Malidiya, as stated by the game itself.
Temen 👉 Suhu
Temen is simply Sumerian for foundation. Whatever Akkadian-speaking polity there would be over there at the time would be called Suhu.
Suhu 👉 Khana
Tutub 👉 Shaduppum
Tutub was barely, if at all, inhabited at that point.
Sippar-Amnanum 👉 Kazalla
Sofia put a city on the wrong side of a river again. Kazalla was in the area and is not discovered.
Ekurma 👉 Arrapkha
Firstly, It’s Ekurmah or Ekurmakh. Secondly, Ekurmakh was about 220 miles to the south of Arrapha.
Nineveh 👉 Ninua
The era-accurate name.
Shibaniba 👉 Sibanibe
Lullumu-shaplu 👉 Lullumu
Lullumu-elu 👉 Turukkum
The Northern Oasis Fields 👉 Irepdjezdjez Vineyards
Changed the Anglicisation of the ḥ sound to h (for instance Horenpi rather than Khorenpti) because ḥ is not ḫ or ẖ. Also replaced a duplicate of the name Horenpi with Wenennefer (this name was completely missing).
Pa-Wehat (faction) 👉 Yam
A lost nation in the area that left no trace except a dozen references in Egyptian chronicles.
Pa-Wehat (place) 👉 Wehat
Cauldron, the original oasis from which all other oases derive their name (including the very word oasis). I removed the definite article because it seems redundant.
Kush 👉 Kash
Kash 👉 Kush
Because Kash is the Egyptian spelling, so the Egyptian-controlled faction Kush should be Kash.
Tsont-nofre 👉 Paihuty
Tsont-nofre is a female name, and Paihuty, a known Libu name, was missing.
Tjehenu tribes have received their actual attested names.
Per-Sumura 👉 Demi-Usermaatre
Literally Ozymandiasville, the closest we've got to an actual Egyptian name for this place. The full original Egyptian wording of this place name is demi-en-Usermaatre-Setepenre, meaning town of Ramesses II; I use a shortened form (like with Mennu-khai-em-Maat/Kha-em-Maat).
Idu 👉 Ihi
Replaced the Assyrian name with the old Babylonian name, but, left the faction Assyrian, to simulate the Assyrian takeover.
Qema/Mefket 👉 Per-iret
Iconic but undiscovered site of an era-defining battle between Merneptah and an international invasion force. Sinful not to have it in the game, just like Djahy.
Anat 👉 Suru
Capital of Suhu. The real Anat is on the opposite bank.
Sapiratum 👉 Anat
Sapiratum isn't actually discovered yet, and it is not even known if it is not identical with another place name; unlike Anat.

Still no idea what to do with the rest of the incorrectly placed settlements along the Euphrates.

Replaced Olophyxos with Thussos because Olophyxos is on the opposite side of the peninsula in real life.

Olophyxos (faction) 👉 Mugdonia
Boeotia 👉 Gwoötia (reconstructed Proto-Hellenic form)
Athens 👉 Atheëneë (ditto)
Attica 👉 Atthikeë

Rearranged the islands and the tribes of Ithake to be in line with contemporary research on Homeric Ithaca.

Reverted the Egyptian unit names back to more conservatively Anglicised forms because some players were struggling with them. Should perhaps release the Egyptian names as a separate Workshop item.

Apesh 👉 Per-Sumura

The westernmost Egyptian frontier ever. We know not its real name, but, we know it was a fortress either built by or at least active under Ramesses the Great, we also know he settled a bunch of Canaanites in the area for one or another reason (which resulted in attested sites of temples of Canaanite deities), and the contemporary name of the neighbourhood where the archaeological site is located has got a very peculiar name that can be roughly translated as ‘vulture mother’s rest’. All these details come together neatly to allow for an Egyptian name that draws from Canaanite myth as well.

I fear this is the final update for the foreseeable future.

Tentatively reconstructed a possible Napatan name for the person the Greeks called Memnon.

Gave Ithacan Exemplary Ambushers a historically fitting Archaic Greek name.

Corrected a couple orthographical mistakes.

The in-game Sangarian Phrygia is nowhere near the Sangarius. I have renamed the faction that actually occupies the banks of the Sangarius to the Homeric name of the Phrygians who lived there, the Mygdonians. Sadly, in the process, another, historically attested local tribe the Mariandyni has had to go, while Sangarian Phrygians become a non-playable faction. On the other hand, this leaves room in the area between Apasa and Hapalla, which was historically at least in part Proto-Lydian land. The playable faction in this area is Proto-Lydians now, named the Meonians, as ancient authors agree the Meonians were the original tribe that came to be known as the Lydians in the Classical era.

I assume the contemporary Arabic name might come from the Nubian word for bow, tungul. The devs evidently agree, because they made this faction specialise in ranged warfare. However, while a place called Tungul is real and historical, it is a different place, found hundreds of miles away from this oasis, and in all historical documents the oasis in question is known from the earliest times simply as ‘Wehat’ (literally ‘Oasis’, with no additional specifics like with all the other oases; it is not impossible that the very word oasis (Greek word that comes from the Egyptian wehat) originates as a proper noun for this place). There’s also this notion that the modern Dunqul oasis is what Ramesses’ foreign lands list means when it refers to a Mairi, but Mairi might as well be in Nubia for all we know, so ‘Pa-Wehat’ (‘The Oasis’) it is.
This is the most popular transcription; more precisely Duaut-neferet but I feared it would not be as punchy. The place, as opposed to the faction, has received the more orthographically pedantic version of the name though.
In real life, Nedjfet was two provinces: Nedjfet-khentet and Nedjfet-pehtet (Upper Sycamore and Viper and Lower Sycamore and Viper), and Zawty was the capital of the former. But in the game they are sort of fused, so I am eliminating the division and presenting a fused version of Nedjfet. Because it would be odd to have only Nedjfet-khentet and no Nedjfet-pehtet.
Seeing a Ra-ked not surrounded by water on two sides is as jarring as it would be to see a landlocked Manhattan. The nearby settlement Demi-en-Hor, (in addition to being the real capital of the province Ra-ked was part of) although also situated on the shore of (gargantuan and astonishingly, completely absent in-game) Lake Merit, only bordered water (Lake Merit) on one side, whereas for Ra-ked, Lake Merit functioned as one border of the settlement and the Mediterranean as another. In real life, Demi-en-Hor sort of still had access to the Mediterranean through Ra-ked on Lake Merit as well as Per-kaut directly on the Mediterranean shore, with Ra-ked and Per-kaut serving as a ‘gates’ between the Mediterranean and Demi-en-Hor, perhaps in a manner comparable to the Piraeus-Athens relationship. I have decided to turn Ra-ked into a Pharaoh equivalent of Rome II’s Athenai, that also did not actually border the Aegean in 272 BC but is portrayed in Rome II as a port, with Piraeus and Athens fused into a single settlement.
Sofia put Per-Ramesses meri-Amon in a completely incorrect location; Mennu-khai-em-Maat, the Egyptian seat of power in Nubia under Amenhotep the Apostate, stood closer to where Sofia put Per-Ramesses meri-Amon. Amenmesse’s capital being in this location could’ve been something that happened historically because chances are, he had to flee or otherwise never managed to secure Lower Egypt due to popular resistance to his Atenist revivalism, part of which could’ve been the restoration of the Atenist capital of Nubia. All of this is pure conjecture, but it works for the purpose of the mod.
The legendary now-lost original capital of Upper Egypt and, in 1205 BC, still not lost and the actual real-life capital of the province. Abdju is in turn ‘demoted’ to the secondary cult centre it was in real life (the unique outpost in the region still refers to Abdju so it serves as both the Abdju temple and as Abdju itself).
Peculiarly, the real settlement in whose place the fictional Ur-gem stands was called what translates to ‘Large Stone’. The devs either accidentally put a stone settlement in the correct place, or knowingly added Dehenet Weret to the game but gave it a made-up name for some reason.
Undiscovered location in the general area, mentioned by Ramesses IX.

The real Nahita is further to the south, but at least the directions between Tuwana, Nahita, and Puruskhanda are preserved.
Luwian name for a place where most people (most likely) speak Luwian.
Unfortunately, Sofia’s ‘Malidiya’ stands in Isuwa, whereas the real one is in Karkamissa.
The idea that the place name ‘Khantap’ has a Nesite etymology is dubious, meanwhile the nearby attested Warsuwa is not represented.

The real Hazor is on the opposite bank of the Jordan; in the game, the place is an outpost slot in Tzur’s region. As for Yenoam, it’s often mentioned, no one knows where it was precisely, but most hypothetical locations are in the area of Sofia’s ‘Hazor’.
A town belonging to the kingdom of Jerusalem is mentioned in Akkadian documents; the town’s name is given as Bit Ninurta. Because ‘bit’ is ‘house’ in Akkadian and Ninurta is an Akkadian god-name, but the town is supposed to be in Jerusalem’s territory, I suspect that the attested name might be a ‘localisation’ of an unattested Canaanite name into Akkadian, so I would like to ‘localise’ the Akkadian name ‘back’ into Canaanite as Bayt-Athtar, but for the purpose of sticking closely to sources I am leaving the exact Akkadian spelling.
The settlement name ‘Sukkot’ is either altogether exclusively biblical or a distortion of the settlement Sofia named ‘Tjau’ (which is not its real name). Thanks to astronomically improbable chance, the Vatican Library preserves two copies, in Arabic and in Egyptian, of the same text that refers in passing to a town in the exact spot where Sofia put this ‘Sukkot’, and it just so happens that in the Egyptian version of the text, the name of the town is completely different and appears to have an Egyptian etymology.
The name of the settlement Hetch, the settlement Hetch itself, and the faction Hetch that inhabits it are all imaginary. The closest attested real-life coastal settlements in the area are far to the south and to the north. The War for Irethorru’s Armour papyrus mentions an otherwise unattested ‘port’ called ‘Nayker’ that I could use, but I personally suspect that ‘Nayker’ is simply an idiosyncratic spelling of Naucratis, which is supported by the events of The War for Irethorru’s Armour taking place in Lower Egypt. Sofia’s ‘Hetch’ is too close to the shore to be Per-Hut-Hor, and a food settlement rather than a gold or bronze settlement, but Per-Hut-Hor is the only known place-name from the area aside from the more general ‘Mefkat’, so I think there is no other choice but to conflate Per-Hut-Hor with its port (whose name is either unattested or attested on an obscure unpublished ostracon I haven’t seen) à la Rome II’s Athenai.
Undiscovered seat of Egyptian administration on the peninsula; in real life was probably situated a tad (about a hundred miles) further to the south.
Sofia’s in-game ‘Timna’ is further from the real-world itself than Sofia’s ‘Hathor’. We know nothing about Rakhet other than that it’s somewhere on the peninsula.
Area of mining of some shiny ore, also given as Ihuiu or Ahwaw. Its most likely real location is in the general area of Sofia’s ‘Deshret Reithu’, but that settlement hasn’t anything to do with shiny ore, so I am putting it here.

The faction Rhacotis is made-up; its territory mostly overlaps with the real Egyptian province Wa-em-huu-ament. Because there is no Wa-em-huu-iabet in the game and no room for it, I am leaving the name of Wa-em-huu-ament just as ‘Wa-em-huu’.
These gentlemen appear all over the place and haven’t a concrete homeland. ‘Libu’ is a bit more specific than ‘Tjemehu’ and refers to the new area added in Dynasties (not too fittingly named Tjehenu as well) while ‘Tjemehu’ borders on mythological and refers generally to western invaders.

The Phrygian name for their country centered at Gordum city.
Tribe with convoluted lore variously regarded as either the direct European ancestors of the migratory Phrygians who founded Gordum, or the original name of the migratory Phrygians who founded Gordum, or a related but different tribe, or a completely unrelated tribe or tribal group. I am depicting them as a migratory ‘tribal pool’ out of which the different settled Phrygians emerge.
By 1205 BC referring to the city as ‘Kanes’ was the equivalent of saying ‘Looteckia’ when you mean Paris today.
The devs threw two Hubisnas into the game world: one in the correct location, but called Cybistra; the other – in a random spot between the real Hubisna and Tarhuntassa, and called Hubisna. I have used the name of an undiscovered city from the general area for the fake Hubisna.

Baffling how of all ancient place-names this one is not in the game, while perhaps Ramesses’ greatest real-life military achievement contains it (‘Battle of Djahy’).
Name of a mining town somewhere on the peninsula. Sofia’s ‘Nekhel’ is not a mining town strictly speaking, but bronze smelting roughly

Same thing but in Egyptian.

The Nesite name the English ‘Highlands’ is a direct translation of.
Ditto.
There is a hypothesis that this particular settlement, Dusae, literally did not altogether exist and is a scribal error for a different place name. In any case the name itself comes from documents from a much later era, so I’ve decided to replace it with Tuhupurpuna, an undiscovered Bronze Age settlement that is hypothesised to had existed in that general area.
Another of the bizarrely placed settlements in this game. Puruskhanda’s precise location isn’t known, but in any case it’s supposed to be on the opposite shore of Lake Tatta.

Real-life Egyptian sources refer to Irsu as ‘a Kharu’. Even though originally it meant a specific ethnicity, by 1205 BC it meant more or less ‘Canaanite and not from any well-known nation’. It could theoretically indeed be someone from Palmyra. Given his emphasis on raiding and ‘forced labour’, I am inclined to equate his faction with notorious Canaanite-Mesopotamian raiders, mercenaries, and all-around miscreants who at least on one occasion attacked Tadmar and could’ve theoretically controlled it around 1205 BC the Shetiu, but Sofia themselves have added the Shetiu as ‘Sutu’ to the east of Palmyra. Another tribe or tribal group that might be related or might not be that related to the Shetiu in the area was the Akhlamu, but Sofia chose to portray them as also living beyond the area Irsu occupies and as unrelated to either him or the Shetiu. There is no choice but to simply go with the attested Egyptian term for what his nation was.
It might be too early for this kingdom but there is no evidence that it totally did not exist around this date either and the game is already part Iron Age anyway.