I know, especially if it's fixing bugs or flaws. Even asthetics or performance enhancers, if it's still under warranty, flash it for free. It's part of the overall service id think.
Several hours? Holy shit, that's not good, sounds like there is something going on that needs some babysitting. Hopefully there are no major issues with the new flash. TBH I have seen this with many complicated systems, shit has to install, then it has to think thru some crap, calculate through some other shit, figure out new numbers, reflash those, see what it shakes out, re calculate, and go through algo's that are just obnoxious just to get to a final output. It's not just, throw this new software on, stuff has to be integrated.
GE was notorious for that as well..
Aaron