You say that the natural draft furnace is already designed for H2, NG and LPG.  So it is safe to assume that the furnace already has flame safety equipment for each individual gas train.
 
Also, it is assumed that the injection lances are separate for each of the fuels, since the switchover will be done on-line.  So the only adjustment that is required is the amount of combustion air.  The combustion air should be adjusted depending on the amount of the fuel used.  The controller for combustion air should be programmed accordingly.