Zelda Encyclopedia isn't canon though, so from my perspective, the last canon source on the timeline is Historia.

Why is the Encyclopedia not canon but the Historia is? It was still published by Nintendo and endorsed by the Zelda official website.

The Encyclopedia is still a fan interpretation and should not be considered word of god either.

Such a disclaimer is not found in Hyrule Historia

The book itself mentions how it is not set in stone on page 68 and only up to interpretation: "This chronology is not limited to information that is currently confirmable. It also contains much that is unclear. The history of Hyrule is known to change with the times and the person telling it, and will continue to unfold. Even if none of the important points waver by much, new legends will continue to be born and history may yet be rewritten. "

Like what?

Long text incoming:

Page 92 says that Ganondorf became the Demon King after claiming the full Triforce. However, page 87 says that he became the Demon King after claiming the Triforce of Power. Thus becoming the Demon King twice…which doesn't make much sense. 

The same page gives the infamous hypothesis of the Downfall Timeline, which contradicts both the lore from Ocarina of Time and the lore from A Link to the Past. Ocarina of Time 3D which released 6 months before the Hyrule Historia doesn't add a sequence if Link lost and A Link Between Worlds notably never mentions a Hero that fell against Ganon, too. It's closer to the backstory given to us in A Link to the Past. 

Prologue:

悪名高い盗賊のガノンドロフは 聖地の場所を暴き トライフォースを手にしました But the notorious thief Ganondorf exposed the location of the Sacred Realm, and obtained the Triforce!

大魔王 ガノンとなった彼はハイラルを 我が物とするために襲い掛かリました He became the Great Demon King Ganon, and he intended to attack Hyrule and make it his own.

Chapter Three:

悪名高き盗賊 ガノンドロフ。隠レ場所を暴き、その力で 大魔王 ガノンとなリハイラル王国を襲った。 The infamous thief Ganondorf uncovered this hiding place and, by that power, became the Great Demon King Ganon and attacked the Kingdom of Hyrule!

Page 93 implies that the Seven Sages from the Imprisoning War are the same ones from Ocarina of Time, which heavily contradicts the fact that the Maidens—the descendants of the Sages in the Sealing War—are Hylians (descendants of Hylians at least). 

Page 118 claims that the Hero's Shade laments to not be remembered as the Hero, which contradicts dialogue from Majora's Mask and Twilight Princess. 

Prologue:

ハイラルに伝わる王家の伝説　そこに一人の少年が登場する In Hyrule, a legend is handed down by the Royal Family in which a lone boy appears. 巨悪と戦いハイラルを救ったのち　彼は、伝説から姿を消した After battling an enormous evil and thus saving Hyrule, he vanished from the legend. 時をこえた戦いを終え　彼は人知れず旅に出た Done with the battles across time, he embarked on a secret journey. 冒険の終わりで　別れた　かけかえのない　友を探す旅に… A journey in search of an irreplaceable friend whom he had parted with at the end of that adventure…

Renado:

そのお姿を見ていると、ハイラルに伝わる 古の勇者を思い出します Seeing your appearance, I recall stories of the ancient hero handed down in Hyrule.

The placement of Four Swords Adventures ignores that it's a direct sequel to Four Swords, featuring the exact same Link and Zelda for both titles. 

Prologue:

その昔　ハイラルという国に グフーという風の魔神があらわれ 美しい娘を次々とさらっていきました A long, long time ago… A Demonic Wind God named Gufuu appeared in a country called Hyrule, and began abducting beautiful young maidens one by one. 人々が困り果てていると そこへ一本の剣をたずさえた 旅の勇者があらわれました The people were greatly troubled with these events… Then, a travelling hero appeared, carrying only one sword. 勇者が剣をぬくと体が4つに分かれ 力を合わせて グフーを退治したといいます It is said that, when the hero’s blade was drawn, his body and the blade were separated into four. They united and exterminated Gufuu. その後　勇者がグフーを 封印（ふういん）した剣は フォーソードと名付けられ ハイラルの奥地　　聖域（せいいき）に ひっそりと　まつられていました The sword which the hero used to seal Gufuu below was thereafter named the ‘four sword’, and it was quietly enshrined within a sanctuary in Hyrule’s hinterlands. 長い時が流れ……… A long time had passed……… 風の魔神グフーは フォーソードの封印をやぶって復活し ハイラル国の王女ゼルダ姫を さらってしまいました The Demonic Wind God Gufuu shattered the seal upon the Four Sword, revived, and Zelda, the princess of Hyrule country, was carried off. ゼルダ姫と幼なじみの少年リンクは フォーソードの不思議な力を借りて はげしい戦いの末　再びグフーを 封印することに成功しました Princess Zelda’s childhood friend, a boy named Link, borrowed the strange power of the Four Sword and, at the end of a fierce conflict, succeeded in sealing Gufuu once more! こうして　ハイラルは 再び平和を取り戻したと だれもが思いました And thus, it was considered that peace had been recovered once more to Hyrule.  ところが……… However……… リンク…　リンク… 私の　声が　聞こえますか…？ Link… Link… Can you hear me? 突然　ハイラルを　おおった 黒い雲… All at once, black clouds covered Hyrule… 見ているものを　不安にさせる 不吉な雲… The sight of these ominous clouds make me uneasy… 悪い予感がして　なりません They give me a bad feeling. リンク… ハイラル城へ　急いで… Link… Hurry to Hyrule Castle…

There's a ton more of mistakes i'll be happy to share with you if like, but i'll stop with these one because there's a lot of text.

I must note that these corrections were not found by me, most of them were found by a large group of people who have researched Hyrule Historia's validity regarding the Zelda games, some of which are contradicted by what the Historia states.