So I followed all the videos for “How to Build a Raspberry Pi Drone” using the Navio 2 shield. I haven’t faced any problems in all the videos until the video “First Time Flying Drills/Advice”. I would give my drone full throttle and the motors run with which I am assuming max rpm (max thrust), but the drone itself is not getting off the ground. I don’t understand why. Is it because I am flying in an area colored as red in Mission Planner? Or is it because I removed all the ESC red lines that are connected to Navio 2? One of the videos said to remove all but one, but I decided to remove all after one of them started smoking which had the red line to it. Or maybe neither of those are the reason…any thoughts…ideas? I am a high school student and a first-time droner so the issue might be simple but I am not experienced 
Also, just to note, I am also having an issue arming my drone using the RC controller (throttle down and to the right for few seconds if I am correct), I have been arming it using mission planner where it has a button to arm and disarm the drone. I don’t know if those two issues are related but its worth mentioning.
Drone not taking off?
An esc is sometimes used to (optionally) power the servo rails with +5v if you want to power a device, eg, servo motor. So removing all of them is ok.
The FIRST issue you need to address, however, is why there is a short (ie, creating over-heating and smoke). I would not recommend moving forward until this is fixed. There might be a small piece of conductive material in the pins or in the Dupont connecter that needs to be cleaned out.
The MP red zone will not disable flight. What is your All Up Weight (AUW) with batteries?
What is the radio pwm range after calibrating the tx sticks? I would recommend re-calibrating the escs.
Don’t know why arming with the stick is not working, but what is the fc color code showing and what audible feedback are you getting? Are you engaging the safety switch? Check the pre-arm settings as well.
btw, you will find this hobby is one of constant problem solving. I would recommend becoming familiar with the resources at ardupilot.org.
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Agreed with @jax200, definitely look into why you experienced smoke on that ESC. Could be just a bad ESC or a short somewhere else as @jax200 suggests.
Keep going @ali1almakhmari ! I know how frustrating it is first starting out, this drone hobby does have a way of challenging us 
1st: @jax200 20 points