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I have an answer to one of the questions (link) and many comments were there. Now every comment disappeared while the comments under the other responses are still there.
What might have happened? Is it a Stack Overflow bug or someone deleted them intentionally?
Next time, please ask about site-specific things on that site's meta. In your case, since you are asking about Stack Overflow, that would be meta.stackoverflow.com. This site, meta.stackexchange.com, is the meta site for the entire network, so if your question only pertains to one site, then it should not be asked here.