I'm guessing this is not a S3D setting but part of your printer profile? I have a Felix TEC 4 and the default there is PLA left, PVA right. Now, my printer comes with fans on both sides, so it shouldn't matter for me.
Not sure this helps you, but these are my 2 cents..
For swapping the material settings, typically I've found that you'll want to confirm that the extruder settings for left and right are swapped, as well as the temperature settings for left and right. Bed obviously can stay the same.