IMHO, you need to use the CN that the government stormwater reviewer will accept, so ask him. Do not try to use "D" as pre and "A" as post unless you are lowering the seasonal high groundwater at least 3-5 feet below grade. Here in central Florida, normal practice would be to use "D" pre/post, unless special conditions exist.
Since this is a stream realignment issue, do you have historical flow/flood level data on the stream? Is there an existing USGS or FEMA or SWMM model? (Runoff CN is just one component of your model - channel roughness, time of concentration, etc are also very important and require some judgement.) Most importantly, how does your pre model compare to historical data and will the regulators accept your methodology?
Clifford H Laubstein
FL PE 58662