I believe yours uses a similar system to that in the K1200LT, servo brakes. This system is self clearing of any faults once they have been corrected. So a flush should not even set a code as I have done dozens of them on the LTs with no issues. Maybe some one with actual 05 GS experiance will chime in but I don't think you have anything to worry about.
2009 R1200GS (Gone)