The 5 min run in or "initialization" is Necessary every time a bike is re-flashed. It is helpful to do another run in once your riding conditions have changed or you have modified the air intake or exhaust. As the computer does have the ability to make changes to improve ridability by drawing information from an altitude sensor a coolant temp sensor an air intake sensor and the throttle position sensor. It will better to reset the ECU to realize all of the benefits of an Run in, however that has to be done by a Dealer with an XC1 tool or with the Optional User setting tool.
Ratman1 I spoke to a Technician at Husaberg about your dilemma, he is trying to get me the correct re-flash that needs to be done to your ECU for the user setting tool to communicate. There is only one. I'm waiting for him to call me back.