Since I run a long-term campaign setting that stretches through the decades and editions, I never overwrite existing lore (that has been used in the campaign). I modify, stretch, and integrate the new lore wherever possible, but in the case of an out-and-out conflict or rewrite, the old stuff stays. Precedent matters. Mind flayers use the lore from the 2e book the Illithiad; beholders use the lore from I, Tyrant; the fact that leprechauns are a cross between pixies and halflings, per the 1e MM, is in; the fact that elves and orcs can't breed, per 1e lore, overwrites any newfangled information to the contrary.
In very rare cases, I might decide that old lore that came up only as lore, but never as an in-game element that pcs saw for themselves, might be wrong. But usually, nope.
An example of integrating the new with the old: when 4e's new cosmology came out, I integrated it by saying that, first of all, nobody really knows how the planes are arranged and both the Great Wheel and the World Axis were mortal interpretations of the same underlying cosmology; and that the Elemental Chaos was just a deeper part of the Inner Planes where the various Elemental Planes mix together. I still use the para- and quasi-elemental planes.