First big question is:
What do the roots smell like? If they smell at all bad then it’s definitely root rot. If it smells spicy and/or vegetable like, then the roots are likely fine and only stained. Another tell is if the roots are slimy. Like snotty type stuff on em, thats rot and bad bacteria. If no slime at all on top of no bad smell, than yeah the roots are just stained and you don’t have to worry about anything.
For all the talk of Hydroguard and other beneficial bacteria… my experience is it’s all garbage/lies. Have to run sterile or you will eventually have rot regardless. I mean you can run a chiller and never have a problem, not need anything, but if you don’t, you will have rot at some point even if you dump a whole bottle of hydroguard into your 5 gallon bucket. It won’t help, it won’t stop it. It might help your plants maybe, but not in a way that’s worth the money they charge for it.
And poolshock is right out. Saw tons of people all over it the last couple years and how great it is so I bought into the kool-aid and tried it for a few months. In my experience every time I used it, the plants HATED it. I had a plant literally refuse to put any roots in the water for a month solid as long as that poolshock was in there. She would just keep bushing out at the net pot and no roots would get longer than an inch into the water. Soon as I got rid of the poolshock within a day there was roots in the water.
What fixed rot for me, was bleach. Regular ~8% Clorox bleach with NO additives. Dose 0.2ml/gallon every 3 days(72hrs). Plants didn’t care at all, tons of roots everywhere, bud is dank, and no rot at all. No problems whatsoever, and it’s cheap and easy to get and dose.