First let me say that I know absolutely nothing about JDE.
With that in mind, let me ask this question. Why are you doing the reorg in the first place? I remember doing them on the System/38 back in the late 80’s but have not done one on the as/400/iSeries/i5 since I started on it in 1990. Is this a JDE requirement?
Since the time needed will be directly proportional to the size of the file and the config of the machine, my recommendation would be to examine the files in the job stream and only reorg those that were absolutely necessary.