I think it may have happened more recently as well with Ava Marie Ziegler who won Budapest and came to Skate Canada.The wording on that passage in the rules are confusing to me. I interpreted is as the Challenger winner goes at the bottom of the top 10 names....?
I can only recall it happened once. It was in 19/20 When Makar Ignatov won the Nebelthorn Trophy and then later got a replacement spot at NHK Trophy. Ignatov was injured the season before so he was never on the SB list initially.