FAR fuel requirements tend to apply to planning, usually before you go but could apply to in-flight planning...for example if the DEST goes down while enroute and now you need an ALT, at the moment you select that ALT, you must meet the usual alternate fuel requirements. But in the split second after the ALT is officially designated, you can do whatever the heck you want as long as it's reasonable and rational and not 91.13-ish.

Basically the FAA wants you to have a practical plan and the fuel to execute it before you go. Once airborne you can adjust as desired.