Did any characters that appear in both parts of FE4 not get merged?
From what I can tell, Finn, Oifey, and Shannan all got merged.
Assuming the list I found is accurate, the characters who didn't get merged were:
Hardin (Coyote and Dark Emperor listed separately)
Camus (Camus, Zeke, and Sirius all listed separately)
Tiki (Adult Tiki listed separately)
Briggid (Eyvel counted separately)
Marcus (Blazing Blade counted separately)
Eliwood (Blazing Blade counted separately)
Bartre (Blazing Blade counted separately)
Karel (Blazing Blade counted separately)
Guinevere (Blazing Blade counted separately)
Zephiel (Blazing Blade counted separately)
Merlinus (Blazing Blade counted separately)
Owain (Odin counted separately)
Inigo (Laslow counted separately)
Severa (Selena counted separately)
Anna (All versions counted separately)
So basically it seems like the separated ones have different names (Camus, Briggid, Owain, Inigo, Severa), or are straight up different people (Anna).
The remaining leftovers are Hardin (who's a radically different character depending on if you're talking about pre- or post-possession), Tiki (who's 2000 years older and finally an adult), or the Elibe crew (20 years changes a lot).
The thing that makes it weird is that the gap between Genealogy generations is about the same length of time as the gap between Blazing Blade and Binding Blade, so in theory folks like Finn and Oifey SHOULD be separate.
The main difference however seems to be when there's a
radical difference across two DIFFERENT games. So because Three Houses is just one game, it likely won't get its vote split for pre- and post-timeskip.