I'm seeing root rot in one of my mini phals and I just re-potted it from sphag to hydroton.
It had some rotting/rotted roots that I removed when I re-potted it and I left one that was kinda rough looking and it got worse.(black and furry)
Is it the right thing to do to take it out and remove when I see this happening? I think it is but I know stressing it out from potting and re-potting isn't ideal either.
Ray said recently on another post that in semi-hydroponic he would leave it, eventually the roots break down enough that they flush out of the hydroton.
Are you doing S/H or just plain hydroton. I would guess that even using plain hydroton it would be Ok to leave provided you water by letting enough water flow through the pot, thus carrying away debris. That's just a guess though.
If the velamen is soft and mushy, I gently pull it off with my fingers, leaving the root string. If nothing else, these roots help anchor the plant. The roots themselves don't easily decompose, and I want to minimize fungal sources in the pot.
I would just leave it how it is- kinda like Rosie and Ray (in another post) have said. After a period of time, many roots will die off as other roots are "born"- this is natural. If there is just a little bit of "mushy part" on a root or two and there are still other roots that are doing okay, I think you should be fine. If you are really that worried about it, you could treat with a minor fungicide or a bleach solution (somewhere in the ballpark of 1 part bleach to 9 or 10 parts water).