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He posted a reply to his own comment.

Actually, my reply was to Folcon. HN simply doesn't allow you to reply to comments beyond a certain depth sometimes.

Perhaps mods have the ability to extend this for active discussions and that's why I can reply now?

it's timing based. you can always reply by going to the permalink of the comment you want to reply to.

Couldn't reply to this comment - but sure enough, the permalink gives me the option. Thank you for the info!

Yeah, it's a somewhat well-meaning feature (supposed to slow down flamewars) that is extremely unintuitive