One of the alleged Bible Contradictions you will see thrown around is Hosea 8:13 and 9:3-6 saying that Ephraim will return to Egypt while Hosea 11:5 says Ephraim will not return to Egypt.
It’s one thing to look for these between different books with different human authors, or a book really big in scale that’s easy to imagine as older texts awkwardly patched together. But Hosea is clearly a complete stand alone coherent message that obviously says these seemingly mutually exclusive things intentionally for a reason.
However most Apologists have decided to reconcile these texts in a way where only Hosea 11 is true at “face value” because everyone’s thinking is dominated by the popular simplified narrative that the fate of the Northern Kingdom was entirely being carried away by Assyria, or counter to that deconstructing the idea of an Northern Tribes exile at all.
The problem is it’s Hosea 8 and 9 that are Prophecies of the then near future while Hosea 11 when read in its entirety is about the Past but also the far Future when Israel will never be disobedient again. The present tense language is poetic or even ironic, it’s about God having protected Ephraim from returning to Egypt in the past. But the allusion to a future Captivity in Egypt is itself kind of in Hosea 11 in verse 11.
When you read carefully the accounts of the Assyrian Captivity you’ll realize that in spite of occasional hyperbole none of them are actually about the entirety of The Northern Kingdom. 1 Chronicles 5 talks about Pul carrying away just the Transjordan Tribes,, 1 Kings 15 talks about Tiglath-Pileser carrying away just Naphtali, and 2 Kings 17 is just the Capital City of Samaria which was in territory allotted to Manasseh. The proper allotment of Ephraim isn’t included in any.
Instead 2 Kings 17:4 says that Hosea sent messengers unto So King of Egypt. The word Pharaoh comes from a word for the royal palace of Egypt’s Kings yet The Bible uses it often as if it’s a name, I think the same is happening here and So is actually a form of Sais also rendered Sau and Zau which at this time was the capital of the 24th Dynasty. These emissaries may have happened to be of the Tribe of Ephraim and been there when Samaria fell and helped negotiate the city becoming a refuge to fleeing Ephraimites. The 24th Dynasty was short lived but we know little about it's status during the Memphis Based Cushite Dynasty numbered as the 25th. Its status as a haven for Ephraimites could have been maintained.
2nd Chronicles 30 has Ephraimites among both those who rejected Hezekiah’s Passover invitation and those who accepted the invitation. I think the rejectors of Hezekiah’s Passover are the ancestors of the Samaritans. Those who accepted it possibly stayed in Jerusalem, 1 Chronicles 9:3 refers to a time when the population of Jerusalem included people of both Ephraim and Manasseh though the Babylonian Captivity and Return is still documented as being only Judah and Benjamin with their Levites.
After this came the reign of Manasseh King of Judah who desecrated The Temple with Idols. Those who hold the view that The Ark actually came to Ethiopia through Egypt rather than the Menalik story believe this is most likely when The Ark was removed from The Temple. But I don’t think it specifically came to Elephantine till later. At first it was perhaps these Ephraimites in Jerusalem who recalled their brethren in Sais and helped some Levites smuggle it there.
The Cushite Dynasty was destroyed and Egypt conquered for a time by Esarhaddon and Assurbanipal. Nahum 3:8-1 speaks of the Egyptians being massacred and carried away into a Captivity of their own. But after all that the 26th Dynasty arises from Sai under Psamtik I, his son was Necho.
In 2 Chronicles 35 Josiah among other things orders The Ark returned to The Temple. But we don’t see the fulfillment of that intent like we do other things in Josiah’s speech. No, instead after he is done preparing The Temple he attacks Necho, Necho tells him he is doing YHWH’s will and that YHWH is with him and in verse 22 the narrative voice agrees. I’m convinced that the obvious subtext here is that Necho had The Ark.
The Elephantine Colony were initially mercenaries serving the 26th Dynasty. I am among those who disagree with the accusations that they were Polytheists. After the Elephantine Temple was destroyed some stayed and some went to Tana Kirkos.
Bishop James Ussher in the 17th Century interpreted Psamtik I as fulfilling at least part of Isaiah 19 and he didn’t even know about the Elephantine Temple. The “Midst of Egypt” is often looked for in the Memphis/Giza area because people want to read it through the lens of the Upper-Lower Egypt divide, but in antiquity I don't think people outside of Egypt thought too much about that. No this Hebrew word for Midst as a geographical term in the context of Egypt I think most likely refers to The Nile.
Josephus in Antiquities Book 11 Chapter 8 Section 6 possibly alludes to Samaritans being settled in Thebes. What’s said about the Samaritans and Sanballat in this part of Josephus is tied up in Anti-Samaritan Propaganda so I take it all with a grain of salt, but it’s worth noting. Since Sanballat is called a Horonite it’s possible he had nothing to do with the Samaritans as Josephus accuses but was an apostate Ephraimite leader.
Later in Book 12 Chapter 1 Josephus talks about Ptolemy I settling both Judeans and Samaritans in Egypt. Book 13 Chapter Section 4 refers to this Samaritan presence in Egypt again. A Law issued by Theodosius I on February 18th 390 AD shows there were still Samaritans in Egypt then.