I scrub the blade down with baking soda to remove the excess black oxides. If that makes the blade too light color, I rinse well and give a very short dip in the FC again. Then I can finish as normal after washing the blade well.
As said, the black is not harmful. Remember to neutralize and rinse the blade well after etching or you may get unwanted rust spots later on. Use Windex or TSP to clean the blade well, scrub with baking soda, or boil for 10-15 minutes in water with a teaspoon of baking soda added. The boiling also seems to make the black stay better.