Help! Root rot in 3rd week of flowering. How can I make it go away??

Hi,
My plants are in their 3rd week of flowering in a homemade aero system. The plants themselves are awesome, looking great. When I flushed my reservoir this weekend I found that there has been an obstruction in my drain, causing a buildup of water in my aero tub, where the roots were. It's like a light brownish and slimy. I fixed my drain issue, but how do I get rid of the nasty slimy stuff on my once pristine roots? The buds just started popping, gulp, so I am stressin'. Any help would be appreciated.

cut the rotten parts off with clean scissors

what was obstructing your drain?

i think hydrozyme whould help fix that..but not sure

I've been cleaning/flushing my reservoir weekly, last week I saw that my roots were starting to grow down my drain, so I cleared them, thought anyway. So when I checked my tub this weekend I saw like 2" of water in the bottom, and then found more root lodged in my drain. This is my first aero grow, so next time I'll make sure the roots can't go south.
So I should like cut off all of the slimy part of the root? What if it's a lot? Oiy. Thanks much for your replies.

if the water was only 2 inches high it wont be a lot. cut them they will be fine its the only thing to do. it might slow growth a little but if you dont remove them it will spread and get worse. even the regular gardening forums say to cut the roots if their rotten...... google it if you dont believe me