That is a nutrient lock out for sure. Yes you need to flush your whole system.

My concern is starting in dirt then moving to hydro. You may find the roots have slime over them that is causing some of your problems. There are some bacteria in dirt that is not present in Hydroponics you may be dealing with. Smell your roots, I know that sounds funny but it works. If there is root problem you will know.

Add some hydrogen peroxide 5ml for each gallon of water even to your flush. Then add it again when you mix up your new nutrients and balance the water. Are you using tap water or RO water? Tap water will have chlorine in it and that is not good for plants.