The method of watering will not mess up the roots. We just need to decide on the best way to handle what is going on. I would keep them in veg until they recover and hopefully by then you will have a plan in mind for the flower room. I am not a DWC guy nor have I done a flow n grow, I do grow in rock wool, but I use the little crutons for a medium not a solid block. In your flower room if the rock wool is constantly in water an never gets a chance to dry that is what the majority of your issue is. The rock wool needs to dry out. You can top feed them with as much water as you want at a time, the rock wool only holds so much water the rest can just flow back into your res buckets. But you need to let the rocknwool dry out somewhat before watering it again. Thats why I suggested a DWC/top feed hybrid. You may be able to let the roots grow out of the bottom of the pot into your buckets, but you need a way to keep the rock wool from sitting in the water. Even at that, the roots may wick enough water to keep the rock wool wet. That way you will not need to cut up the cube and your roots and you may be able to flower sooner as you wont have to wait for the root system to recover. I would try it with one plant first myself. Try a couple of different things in your flower room to let the rock wool dry out and see how the plant does. Otherwise your going to be looking at cutting up that cube.