If you propose to block up a chimney flue you must ventilate the flue in the room which it once served, usually through provision of a hit and miss vent. Failure to do so will allow condensation to form within the flue with the possiblity of a dirty condensate running down your flue, over time this may leach into the fabric of your habitable rooms. There really is no way around this requirement for ventilation, unless the actual stack were to be partially demolished and reduced to below the roof level (preventing the ingress of moisture).