Disclaimer: This is just my opinion and have no experience to back it up.
Assuming the 50,000 unit is adequate to heat/cool the area, there will probably be little difference.
If the 100,000 unit took 5 minutes to heat the area, the 50,000 unit should take about twice that long.
The area would cool at the same rate with either unit, so assuming it cooled to the set point of the thermostat in 30 minutes, the 100,000 unit would cycle every 35 minutes, the 50,000 would cycle every 40 minutes. The 50,000 would cycle less often, but run twice as long.
Assuming the EER was the same for both, the operating costs difference would probably be negligible.
If the 50,000 unit was marginal for the area, there may be times when it could never catch up and might run continuously. On the other hand, if the 100,000 was way overkill for the area, it may use more energy in the cycling on/off.
Just my $.02 worth. Now an expert can shoot holes in my theory /forums/images/graemlins/smirk.gif