All Sea Doo keys have the same chip in them, and can be programmed in the ECU as any function, Normal, Learning, or Rental. Only the colors are different so you know what it is supposed to be.
If a key is already programmed in the ECU as a Learning key, then the only way to change it to a Normal key is to use Candoopro or BUDS to delete it, then program it back as a Normal key.