This thread deserves attention. After all, your findings are something that I and others before me have also independently concluded.
But I refrained from posting it here because I knew it wouldn't be taken seriously by anyone except a handful of geography lovers.
Anyway, you did so, and I'm quite pleased about that.
Well then, let me show you my detailed juxtaposition of the various places in the three games.
Holodrum:
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44 downloads
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37 downloads(1) Horon Village => Old Kasuto:
Both maps have a town here. Horon could've been renamed Kasuto when the country joined Hyrule.
(2) Samasa Desert => a desert:
Here both maps show a large desert next to the sea.
(3) Woods of Winter => a forest:
Woods can go back or grow denser over time - here they did the latter.
(4) Sunken City => a lake:
Holodrum's biggest lake houses Sunken City, which is possibly still down there by the time of AoL.
(5) Mount Cucco => tunnel to New Kasuto:
One of the many caves in Holodrum's mountains broke through on the rear end. The grove behind the mountains, where New Kasuto will be, are not shown on OoS' map.
(6) a river => a river:
Both maps have a river running west from the great lake.
(7) Eyeglass Lake => a river:
First the river ends in the swamp, later it takes its way through Eyeglass Lake, through the Maku Tree's glade, and just east of Horon/Kasuto into the sea. The sandy path from the cemetery to the bridge (AoL map) may once have been part of the river bed. Thus, the near bridge was in Holodrum the land mass between river and Eyeglass Lake.
(8) western coast => Path of Fire:
Later the pirate ship is gone, but the spooky air remains through the Moa ghosts. In Holodrum the path south of the cemetery was blocked at the western border, but later it runs on to the Valley of Death.
(9) graveyard => graveyard:
Everything matches: north of both cemeteries is the swamp, east is a road running to the river. The Lizalfos' canyon west of the graveyard was not accessible yet in Holodrum.
(10) Spool Swamp => a swamp:
Though not always as big as in AoL, the swamp has been there all the time. In the east it's flanked by the Holodrum Plains which later become part of a forest.
(11) Lost Woods => a swamp:
Later these so-called Lost Woods connect to the swamp which thereby expands up to the mountains.
(12) mountain range => mountain range:
Not much of a difference. What became of Holodrum's Goron Tribe and the Temple of Seasons? Perhaps they still exist unseen during AoL.
Labrynna:
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39 downloads
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27 downloads(1) Crescent Island => an island:
The prerequisite for Labrynna's location is an island south of the mainland, just like the one in AoL with the Island Temple on it. And it even has the shape of a crescent. The temple is at the same place as the Tokay Rock in OoA. The Tokay themselves might have degenerated into Lizalfos and left for the canyon near Holodrum.
(2) Yoll Graveyard => royal graveyard:
Already big in Labrynna, it was enlarged even more when the great king was buried. The Forest of Time gave way to more graves.
(3) southern shore => southern shore:
By the time of AoL, rows of tombstones are reaching till the southern shore.
(4) a river => a river:
First this river took its time to reach the sea. Later a bay originated where the Black Tower used to be. The bridge north of the tower is still in use during AoL.
(5) Rolling Ridge => a ridge:
Somehow the ridge elongated south to the coast where once was Lynna City. In the process, the glade of the Maku Tree disappeared.
(6) Lynna City => coast:
The city vanished completely. It wasn't that big, after all.
(7) Nuun Highlands => southern forest:
Plain and simple, some woods sprang forth.
(8) Symmetry Village => northern forest:
Seems like too many trees have grown in the village. The only house remaining in AoL belongs to Bagu, the strongest man in Hyrule.
(9) another river => path through the woods:
Before Talus River joined it, this river was the original one flowing into the sea. Later on, its upper bed was drained and became a path through the forest.
(10) Talus River => a river:
The upper part of the river from (4), going over the hills.
(11) Fairies' Woods => plains:
Never really dense, these woods became a grassland with some trees remaining in the east.
(12) Black Tower => Great Bay:
Presumably, the Black Tower was torn down, and its base was flooded by the river running from the hills, broadening it to a bay.
(13) Zora Village => Town of Saria:
The Venice-like town of Saria could be have its foundations on the Zora Village that is down in the sea strait. Perhaps the humans intended to name their town after the legendary Zora sage - and got the names wrong.
(14) Zora Sea => foot of Death Mountain:
More land showed up due to a retreat of the sea. To the south, the Death Mountain foothills extend, as seen in the in-game Labrynna map that Mourngriever posted.
(15) southern shore => long bridge:
From the foot of Death Mountain to the southern shore, a long bridge was built across the Sea of Storms. The stormy waters could explain why the bridge is partially broken in AoL.
As for whether the developers intended it or not - no telling. But I wouldn't mind either way, it's been an integral part of my fanon for a good while.^^
It's certainly a lot more interesting than saying, "We don't know where the Oracles countries are located", and, "Northern Hyrule from AoL never made a reappearance".