To flush, just fill your reservoir with water. No nutes.
The point of flushing is to get your plants to use up all the food reserves stored in their fan leaves, etc.
You don't need to pH the water when you flush. pH is only useful for nutrient uptake. Since the idea of flushing is to STOP feeding the plants nutrients (and since you're not adding any, anyways) you do not need to pH the water.
Before changing your res, I suggest you pour water over the ydroton pots. This will flush out any salts that may be hiding in there. When dump your res and fill it with water.
I usually flush a week or two before harvesting.