There seems to be some disagreement about the nature of Shemini Atzeret and the implications of its being called a "Regel Bifnei Atzmo" (a stand-alone festival).
But I assume that, because there are different practical implications (like sitting in the sukkah or ending shiva, both mentioned in the above link), at some point it must have been known exactly what to do. As the article indicates, "The Rishonim disagree as to the implication of “regel bifnei atzmo.”" so what was known became unknown (possibly like the order of parshiyot in tefillin).
Is there any discussion about exactly how and when the nature of Shemini Atzeret became in question?