During the aftermath of the 3rd war and the defeat of the burning legion, The now-Bloodelves were deemed "traitors" by the the remaining Loredaeron survivors' leader and were awaiting their ordered execution, when illidan's Naga interfered to save them. That is why they never returned.
https://wow.gamepedia.com/High_elfThis would hold if all high elves on Azeroth had renamed themselves to blood elves. In fact, I was under that assumption until I started seeing random neutral high elf NPCs in vanilla WoW, which remained as such when Blood Elves became playable in TBC. TBC also had the Allerian Stronghold in Outland, which didn't help sell the "high elves joined the horde" narrative (Blizzard could have made them neutral since both Alliance and Horde were fighting the Fel Horde and Illidan's forces). At that point they were arguably scattered, which was acceptable. Then Wrath came and established that not all high elves became blood elves and see themselves as separate from them (hence why things like Quel'Danil Lodge and the Silver Covenant exist). Given the Quel'Dalar questline and comments from certain high elf NPCs, the high elves and blood elves are not on good terms and are thus not a unified people.
Since then, they maintained an in-world presence and played roles in certain events (the Dalaran Purge, Suramar). So you're right, the story has progressed. And high elves are still very much their own thing and remain loyal to the Alliance.
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"the high elves rejoined with Prince Kael'thas Sunstrider, and renamed themselves "blood elves", in honor of their perished brethren.[8] The blood elves then sought to unite and restore their people to the glory they enjoyed at the height of high elf civilization,[9] and have retaken much of their land from the Scourge.[8]
However, a few high elves did not rename themselves blood elves. High elves and blood elves are physiologically the same race, and the difference between high and blood elves is only political.[10] When Quel'Thalas left the Alliance, some high elves chose to remain with their allies over their kingdom, and to this day still support the Alliance.[7] Some high elves were exiled from Quel'Thalas after the Third War.[11] Other high elf remnants have chosen to rejoin the Alliance in recent years, arriving to a cold reception.[2] Modern high elves are a rare sight, and are commonly mistaken for blood elves.[12][13] In consequence, there are very few high elves left on Azeroth today. High elves did not gather in any significant numbers and are a very small group of individuals. Indeed, modern high elves cannot even truly be said to have a culture—only a past filled with glory and regret.[2]
As a people, the high elves are all but extinct: the remnants of the remnants of a fallen race.[14] Though without any official leader, Vereesa Windrunner leads one of the few organized high elf collaborations, the Silver Covenant, as its self-styled Ranger General. Auric Sunchaser, a captain of the remnants of Alleria's ranger cadre found in Terokkar Forest, serves as the high elven representative at the restored Sunwell in modern Quel'Thalas."
Only some High elves rejoined the Alliance to begin with, and as for the Silver covenant, their true loyalty has been and will always will be to the Kirin Tor (neutral as been confirmed and reinforced by every kirin tor leader. Of course in the instance where the Silver covenant participated in the purge of dalaran, the primarily reason was that they accused the sunreavers of breaking neutrality in the conflict (Mists of Pandaria), more than anything else.