[NepNut]

CJ,
If you wanted the nep to flower, don't trim off. Wait till still it done flowering, collected the pollen / seed then you can trim.

The brown area is usally harder to root. However if you cut off the green stem and left the brown part intact with the roots, you'll have better chance of getting generation of new bud. This is however, very dependent on your growing condition and species/hybrids.