Basically I currently see it like this: If any champion previously lived in the Institute of War, his current location is unknown (of no fixed abode). The are wanderers in the land of Runeterra (similar to how you would have seen Fiddlesticks find Twisted Fate in Noxus all randomly in the cinematics).
Any lore that has no mentioning of the League is still canon. Any lore that has it mentioned is due to be updated or altered (or that specific lore removed due to champions living in the League as I mentioned above).
League Judgements by the themselves are not canon (because there is no league to judge anything), but some info in them is still considered canon if it has no mentioning of the League. The mental evaluations of the characters in those Judgements are still canon (unless the entire main lore has been completely changed which may indicate that it isnt canon, like with Xerath or Trundle)
Nations history and lore is subjected to the removal of any kind of mentioning of the league, after that all of its info should be considered canon until serious lore changes by Riot.