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Let me get this right before I start answering. You have one article having an issue (just one) that is AU and UK, has hreflang implemented, is indexed for keyword searches but not showing for site: searches in Google. Few questions. Have you geo-targeted the subfolders for AU and UK? What version of Google are you using to check indexation? When you say you checked internal links for both, how did you do that? Your own site search (searching on your own site) does not return the UK article? Or do you mean that the site: search is not bringing up the UK article?