I don't know if there is a spot on the ECM memory that stores ALL the "historic" codes or what... but I know how to get rid of the codes to keep the engine light from flashing after you've fixed the problem...
Flip the Run switch on, then while holding the trip / odometer button in, turn the ignition switch to on. You'll see all the lights come on the speedo face, then the odometer will have "PSSPt" with the first "P" flashing. You can cycle through all the letters to find the codes. Once you get to the code, hold the trip / odometer button in until it says "Clear" and that will clear the current code.
According to the web sit it is for "04 and "05 bikes. Probably works on "06 also since it is for bikes with the full serial data bus.
On my "99 it has to be cleared either with 50 starts or with the H-D scanalizer.:badmood: You can read the codes using a jumper in the scanalizer plug, but you can not clear them without the scanalizer. Refer to the service manual, it gives the codes and details on how to read them and what they mean.