Could just be that for the story to play out the 'top brass' have to do that movie/TV show thing of not believing the person telling them what's going on until something else happens to prove it.
Barclay had the same problem once or twice if I recall.
Deadlock comes after Non-Sequitur because I think it was one of the episodes actually made for season 1 which was held over to start season 2 with instead.
Whether Harry was an alternate or not is probably open to debate but for all intent's and purposes he was at least a copy of the original, if not a full alternate.
O'Brien however, was, I believe quite clearly replaced by an alternate after the original died at the end of Visionary.
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist