I have not performed this repair but I have studied video's on the subject for the day when I will need to do this. Go to Dicor's website. They have some very good videos on this and do a walk through for you.
the only reason's you would need to replace the decking substrate is if there are bad spots, then, replace those areas, other reasons, if you want to add insulation, change/repair wiring in the ceiling area etc. This will be an easier access than removing the interior ceiling panels since you assumingly would already have the EDPM roofing removed.
This will be a great subject for the forum. I hope you post pictures along the way and do a step by step review for us. Good luck.