So this has actually happened to me a couple times now. Down in the water I have pretty nice roots, but above the water line I got rot. Has this happened to anyone else? How do you prevent rot where the water doesn't touch?
There use to be a product call DAMP-OFF. I think it was basically sulfur powder. If you can't find that sulphur powder will work or a fungicide of some type.
Damping off off seedlings happens where the stem meet the soil and oxygen and moisture are perfect. With seedlings a 1/4 inch of sand over the soil where the stem comes out can prevent it.
Many seeds have a fungicidal coating to help when the seed is young and at risk of damping off.
Your cuts are almost like seedlings. They are just getting roots and the stem is right above water and is getting stem rot from damping off fungus.