UV the lower plug on a flat engine (as most of them are) faces upward and when you run a cylinder on only one mag, if the non-sparking plug is the lower spark plug it may get slightly fouled with fuel filling up the well between the body and the central electrode. Putting the mags back to BOTH gets all the plugs firing and burns off the excess fuel in the plug. It makes sense to do it for both sets of mags/plugs as:
a/ it is easier to remember
b/ if the upper plug is not firing, it may become fouled also.
If you went from RIGHT MAG OFF straight to LEFT MAG OFF and more than one of the plugs fired by the right mag were fouled then the engine would probably stop.