This is my idea dump to help resolve various lore disrepancies between TR and the canon games, and other projects that make use of our lore, such as Beyond Skyrim.
1) Shad Astula (ESO) and Meralag (TR)
ESO lore: Shad Astula is an academy of mages. Once meant for the elites of Morrowind society and a place where all the Great Houses could study in peace. During the Second Era's Ebonheart Pact, Shad Astula opened its doors to the rest of the Pact (Argonians and Nords).
TR lore: Meralag is a gated community of Indoril.
Headcanon: After the Ebonheart Pact dissolved, Shad Astula became severely underfunded and eventually went under. It is now little more than a basement/ruin under Meralag, full of magical traps, tricks, and artifacts for an unwary adventurer to stumble upon. (Suggestion: create a fun dungeon involving plenty of puzzles and magical items!)
2) Kragenmoor (official games, Beyond Skyrim) and Kragen Mar (TR)
Official lore: "Kragenmoor" is what's referenced in some dialogue in TES3, as well as on maps in Arena and ESO.
Beyond Skyrim lore: "Kragenmoor" gained popularity after House Sadras took over from House Hlaalu. House Sadras incorporated Imperial religious beliefs as well as culture, and now Kragen Mar has fallen largely out of use by the Fourth Era.
Headcanon: Kragen Mar is the proper Dunmeri term from the town, which is often bastardized to "Kragenmoor" by non-native speakers.
3) Bleakrock (ESO, Beyond Skyrim) and Absolutely Nothing (TR)
ESO lore: Bleakrock is an island between Solstheim and the Skyrim coast line. It has Nordic tombs and outposts, though some Dunmer may have settled it in the Second Era.
Beyond Skyrim: Bleakrock remained a Nordic Reaver-controlled island until late Third Era, when the East Empire Company established a small ebony mining colony. After the Red Year, the Redoran took up residence, re-christenizing the island as Bal'Sehrma (literally Bleackrock in Dunmeris).
TR lore: It doesn't exist and never did.
Headcanon: Sometime during the Second Era (but after ESO), another of the Alliances invaded Bleakrock, and set off a magical catastrophe that would send it to the bottom of the ocean. Sotha Sil intervened to save Bleakrock from this invasion, transporting it instead out of space and time. After the Tribunal's fall, Bleakrock reappeared, albeit, probably with some Sotha Sil-esque changes that can be found in ruins or dungeons on Bal'Sehrma. Suggestion: add some ruins to the bottom of the sea in this area as an Easter Egg, and/or some legends surrounding Sotha Sil's doings. More ambitious suggestion: add a questline wherein bits and pieces of Bleakrock start reappearing as the Tribunal's power fades.
Alternative Headcanon (Beyond Skyrim favored): Bleakrock's destruction is something of a Dragon Break. In Beyond Skyrim, the timeline where Bleakrock was saved from disaster is preserved. In TES3, Bleakrock was destroyed. Sometimes these two timelines overlap and blur together. Suggestion: include NPCs confusedly speculating about Bleakrock's existence, as well as varying folktales talking about its destruction and rumored "reappearances" whenever the timelines converge.
4) Davon's Watch (ESO, Beyond Skyrim) and Ildrim (TR)
ESO lore: Davon's Watch is an Indoril town that was assaulted and at least partly destroyed by the Daggerfall Covenant during the Second Era.
Beyond Skyrim lore: Davon's Watch is a small (?) fishing village halfway between Ildrim and Id Vano
TR lore: Ildrim IS Davon's Watch, now a shack-town instead of an Indoril city. Over the development cycle, the name of this town changed to Darnim's Watch, then to Darnim, then to Ildrim.
Headcanon: Davon's Watch was almost destroyed by the Daggerfall Covenant in ESO's timeframe, and never quite regained its former glory, resulting in the town of shacks it is in TR. It was renamed to Darnim Watch after its destruction, and eventually to Ildrim, as the language shifted over the centuries. Suggestion: add a lore book regarding Davon's Watch's history to the game, as well as to the "Ildrim" dialogue topic.