If you include airspeed, throttle or groundspeed changes in a mission
then those should not be saved to EEPROM, as otherwise if you restart
and re-fly the mission you will be starting with different parameters
to the ones you used for the first flight.
This is particularly important for setting the target airspeed when
coming in for a landing. You typically set a low target, but if you
fly again the next day I think it would be a real surprise to find
that your loiter airspeed has then changed to the value from the
landing part of your last mission.
This one can be argued either way, but I think that not saving these
changes is the more conservative choice, and better fits the
'principal of least surprise'