I would start anew. dissenfect with chloride then was with soap and dry. I would probably use the chloride again after cleaning the rez.
Problem is mold reproduces via spores and spores are very hard to kill. there is a chance the spores are coming from a nearby source and your rez is just a nice environment for it to grow in.

If it is 3% it won't harm your plants. Use a cup. I've soaked roots for an hour in 3% without harming them to resolve root rot. Also, Once you start using it, Keep using it. Every water addition and change should have it. Also, i've estimated it only lasts about 4 days so add some every 4 days.

I would go with grizz' suggestion. I had a problem with a fungal growth. I solved by soaking EVERYTHING in 1:10 bleach for about 30 minutes. That will kill most anything. If you feel your problem is serious, you can get a better kill by upping the contact time, and/or the bleach concentration.

I use beneficial bacteria to combat all my fungal pathogen issues.