By removing the red wire from the plug, you are disabling the BEC, so there is no need to remove the black jumper. that's how I've ran all my controllers,
Micro 1895 (had it for 4 1/2 years) BK replaced it with a Micro 2095...I've ran them in this config several years and have never had a problem, ranging from 12 cells up to 16 cells. So if it works with the jumper in but with the wire removed your fine.