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Any Suggestion will be highly appreciated.
You can also find urls that will show a result if you simply paste them into the search box, but never show on the site: operator search. So it's becoming more and more of a challenge to use the site: operator for intelligence gathering.
One thing you can depend on is when a url on your site gets a referral from Google Search - then it's got be in the index. So the most important factor is whether your traffic has been affected.