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Having reported this problem to Emily already, she mentioned to post it here. THere's a bug in the folder settings for a KB article where when ticked, the articles under that folder will show in automatic searches (live chats and tickets). When unticked, it's not supposed to show them, however, it still is, regardless of that option being ticked or not.
My goal is to hide unnecessary folders from searches, however, with the bug, it's still showing folders/articles as results when I don't want them to.