The term "Flush" with regard to either hydralic power steering systems or automatic transmissions is typically a "Fluid Exchange". Usually there are no added chemicals or "flush" additives. A low pressure pump usually pushes new, fresh fluid though the sytem to "Exchange" the old, dirty fluid. With regard to automatic transmissions, there tends to be a lot of old dirty fluid stored in the torque converter, cooling lines and radiator/transmission cooler. You could expect a fluid "Flush/Fluid Exchange" on an automatic transmisson to require 2 times or even a greater amount of transmission fluid that just dropping the transmisson pan for a fluid service.
There are no negative effects of a properly performed automatic transmission "Flush/Fluid Exchange" assuming the proper transmission fluid is used and the level is properly set. Ideally a fluid exchange and a pan drop with a new filter is incorporated as well. Often the "Flush/Fluid Exchange" can be performed while the transmisson pan is off.
The majority of the stories on the Internet where people claim they had an automatic transmission "Flush/Fluid Exchange" then had a catastrophic transmission failure in short order is usually due to the vehicle owner not maintaining the transmission, realizing there may be a problem and then expecting a fluid service to correct hard part problems that were enevidible. New fluid that is of the correct type and set to a proper level will not cause premature failure of an automatic transmission. Usually the pin on the grenage has been pulled long before the fluid service is attempted in a last ditch effort to solve a much more major problem!