The black roots does suggest they are in a stage of rotting....and if too far, so goes the plant. I'd suggest too you instead of the water, use some potting soil--an acidic type, and make peat moss part of the mix. Into the soil, put a couple drops of "No Damp"....a fungicide which will take care of any bacteria the roots might be infected with. Give the plant a good prune back...even as far down as the first node above soil level. The roots evidently were deprived of oxygen being where they were in the water and pebbles. It was good to clean the container and the pebbles but I'd trust more the potting soil and when watered, allow drainage, then dump the excess.

Lucky Bamboo that have spent their whole lives in water may reject soil. Not sure why. Also, my experience is that healthy plants make this transition better than distressed plants. If you want to grow in soil you may want to start with new individual stalks that have not spent years in a rock and water arangement. Make sure you use a container that drains. Start by packing potting soil(I use Miracle Grow Moisture Control) in the bottom of the container leaving about 3.5 inches of space to the top. Set your plants root system on top of this layer. Do not push the root system into the soil. This will make the roots point up. Roots want to grow down. Then pack another 3 inches or so of soil on top of the root system. Lucky Bamboo like packed soil. Keep the soil moist but not saturated with water for extended periods of time. Some drops of Green Green fertilizer may help. Sand helps drainage as well as a layer of rocks at the bottom. Good Luck

To seal it. It keeps the plant from loosing moisture and nutrients from the cut and also keeps fungus and insects from attacking it at the wound. Its a living thing. Just like if you got a cut you would put something over it.

so, i got them out of the pot thing, poured the water out, shook all the jelly ball things out, which were still jellylike and mostly intact, and filled the pot thing a bit more than halfway up with tapwater that was left there for at least 10 minutes before. all their roots are underwater, but i dont know if its enough. their roots mostly looked okay, most of them were either orangeish, whiteish, or slightly brownish. had to tear parts of some off that grew into the ball things. i also thought the balls were discolored because they absorbed the fertilizer for years, but i was told they were greenish and blueish originally. the bottom of their stalk/stem, though, looks totally yellow: and closeup of the older one: this should obviously mean something bad, but both of their bottoms are yellow, and the newer one doesnt show any sign of having a problem at all. well, one seems yellower than the other, but the leaves are all totally green on the newer one, greener than any on the other. so im guessing the yellow part would just have to be cut off? if im right, its not too hard for them to grow roots back. unless they are too weak, and would die from it. i also read that lucky "bamboos" need a special kind of fertilizer. and fertilizer would probably be needed for roots to grow. anyways, i did this days ago, and cant really tell if the yellowing stopped or just got slower. or only seems slower because there are no almost-dead leaves that get yellow in days