Flushing through the tops of the pots will send high concentrations of potentially harmful salts straight back into the root zone. According to autopot if you use the system as intended then a salt layer accumulates towards the top. If your doing it by hand I figure you'd need to dump a few gallons of water in to get out the excess nutrient.
Remember good old tap water is still filled with at least 400ppm of mineral salts too.
Salt buildup will cause too high ec, pH will drift, causing the appearance of nute deficieny.
50 l sounds good.