I do it before I reassemble the generator so that the 3rd brush isn't setting on the commutater. I then jumper direct to the field to flash it.
The book I reference DOES NOT give instructions for flashing. (I stand corrected) Rather they indicate that if the generator will "motor" when connected to a battery, then it will generate fine. Generator/Motor rotation should be "clockwise" as you look at it.
He indicates if the generator will not motor, he puts it to bad contact with the brushes which a couple of "manual turns" clockwise should solve.
He indicates that if the tendency of the generator/motor is to turn "counterclockwise" then the pole/field terminals are electrically "reversed."
He counts on a previously correct and functioning generator, so he never really addresses flashing - which would definitely set things right.
My engineering first guess would be to connect a NEGATIVE (-) battery cable to the lifted 3rd brush, and a POSITIVE (+) battery cable to the generator case. This is, after all, the way the generator poles will live in a Model A Ford all their remaining lives. Moving the 3rd brush only reduces the VOLTAGE across poles to reduce pole amperage/magnetism and in turn reduce (or control) generator output.
It will only take a heartbeat of current flow to re-align the magnetism - so don't leave the connection on lest you burn out the field coil.
Of course if you flash by my method, and find the generator tends to motor backwards, simply reverse the connections used for flash.
Joe K