De-potting plants after a few months :/

I would "clip" off the soft ones (dead) and replant the rest. The plant will probably grow new better roots.

Im not an expert by anymeans, but i dont think i would remove them unless you are sure they are rotting or decomposing. Generaly with plants, roots are only green when they are exposed to large amounts of light. ie "sun burnt" potatoes. I cant really tell from the picture if they look normal or not, but i wouldnt expect them to be green if they werent exposed to light. Maybe just run your fingers through them and throw away any that easily detach themselves. good luck.

I know nothing about aquarium plants (but I'm starting to learn more), but I do know about plants in general. I always dispose of the rotting and/or dead and/or dying parts of leaves/stem/roots because they can carry diseases that will affect the rest of the plant and also (I have read) the plant will use a certain amount of its energy trying to "heal" the dying parts when that energy cold be better spent in growth. So, I think you should carefully cut with a sharp knife (I wouldn't just rip because you could injure other parts of the root system) the dead and rotting roots and then re-plant your baby in your aquarium.

I'm not sure how much of the brown is actually dead or rotting, I would gently pinch the strands and see if they feel hollow or just moosh. If they are firm I'd leave them be, they may not be as new as the green ones, but they may not be dead or rotting.

The cotton like stuff in the pots was most likely rockwool and in the future I would remove the plants from it as soon as possible. It can lead to algae problems in the tank and I don't think it allows for the best root growth. The brown/soft roots were def. dead and the white and green ones are healthy/alive. If you cut them all off, the plant will probably recover, it much just take a little while. I had a sword that was getting really big so I trimmed the roots back to try and control the size of the plant and the plant did fine.

I always depot new plants as soon as I get them home. Regarding the Melon Sword (E. Barthii?) That is in really bad shape. Clipping off the dead mushy roots is a good idea, my E. Barthii is in real good shape and its roots go all over the place now.

There's no harm done. You've removed the mushy rotten roots and I can see from your photos, there are plenty of fresh, live ones. Sword plants put out new root growth real fast. You can trim them down a lot and the plant does fine.