I don't know about separating the algae cells, but I can tell you that F/2 media has about 55 PPM of Nitrate to start with (Math below). Let's assume that your phyto culture consumes only 90% of the fertilizer, then that means your phyto culture has only 5.5 PPM of Nitrate left over. Take that, and then dilute it in the fry tank, and I don't think you have a lot to worry about. You could always test your phyto culture for Nitrates.
Per the , Guillard's F/2 media has 1.0 ml/L of a stock solution that has 75 g
/L of Sodium Nitrate. The Sodium Nitrate has a molecular mass of 84.9949. The Nitrate ion has a molecular mass of 62.0049. So, 62.0049 / 84.9949 of the 75 g
is Nitrate. That means that the amount of Nitrate in fresh F/2 Media is 75 * (62.0049/84.9949) / 1000 / 1000 = 0.0000547, which is 54.7 PPM.