New disc pads require fluid to be pushed out of the calipers to make room for the new disc. I haven't done a brake job in years, but I always bleed the fluid at every wheel. Air in the system can only come out by bleeding the brakes, it cannot dissipate. If you had no brake issues before servicing, I'd look at bleeding the brakes and HCM improperly as the issue now. You can get a HCU code if not properly bleed. Sounds like the dealer wants more of your money.

A SGII can be programmed to read much more than the PCM. Other sites have information that tell you just how to program many other modules. Cleanmpg.com and greenhybrid.com have this information. If you join these sites, you can get a discount on the SGII and follow post on FEH programming for the SGII.