I've flashed the BIOS of my mainboard ( Asus P5W-DH ) last week, but never got any activation issue, the serial I'm using is still counting at 1, the initial activation, so I guess it's quite safe to flash BIOS. However, some mainboards might behave differently, that's why we provide with several spare activations, so people will not need to contact us to use the product, even when the unexpected happens.
Note that, since October 2007, when we first released Zurich using this system, we did only ONE manual reactivation, for a user that got particularly unlucky with multiple hardware failures. And this is out several thousands of orders, this means that basically nobody ran into troubles when upgrading hardware or reinstalling the system.