The flash is done by the dealer via the data link using the Digital Technician; no need to remove the fairing. Iron Cross Audio can do the flash, as well, if you send them your HK radio.
If you're considering the CVO speaker boxes in the fairing lowers, they work with the vented lowers but not the unvented lowers.
I have the HK in my '04 EG with the CVO speaker boxes. Since I sold the Arc 125.2 amp that was driving the speakers in the lowers (I'm waiting for the Rockford Fosgate 300W 4-channel amp), I'm using the rear speaker signal directly from the HK for the fairing lower speakers. Without the amp, the speakers in the lowers are inadequate IMO. The volume has to be raised to near max and the fader set almost fully for the lowers for them to be noticed while riding.
Your experience may be different, of course, using the HK w/o an add-on amp for speakers in the lowers.
Good luck with your project.
Carl
PS: I was very happy with the Arc 125.2 driving the speakers in the lowers with the fairing speakers using the signals from the HK (no add-on amp) and only sold it because of the RF price and 4-channel feature. Adding the CVO speaker boxes was a really good audio upgrade w/ the amp; but, w/o the amp for the speakers in the lowers I would be disappointed.