I am using the latest firmware Copter V4.3.6 and using here3 gps.
I am having an error in the gps heading which does not change its direction along with the nose of the here3. A single gps is being used and the blending has been turned off.
However, the black line of gps heading on mission planner does not align with the nose of the actual here3 and remains fixed at a particular place.
What could be a possible reason for this?
The calibrations are completed.
Not enough horizontal speed?
Could be, but even when the drone is stationary, the gps on mission planner is showing an error of more than 90 degrees, to the actual nose of the here3 gps
The error is there because it is stationary. Not the other way around.
But isn’t it risky with inaccurate gps heading to go for a flight.plus what are the chances that it will align with the flight controllers heading???
You are confusing some things.
Real GNSS heading requires two on board GNSS receivers operating in RTK mode and with a baseline of at least 20 to 50cm.
You do not have that. So there is no way to get real GNSS based heading.
What you can get with a single receiver is course over ground movement direction, and that requires movement.
Thousands of drones world 
wide use a single GNSS receiver and a magnetic compass for heading. That is a proven solution that works fine.
Please explain better what exactly are you trying to solve.
The black line on mission planner is not heading, it is “Course over ground” or “Ground course”. It’s just the direction of the velocity, reported by the GPS. A stationary GPS will report random ground courses, but once you start moving forwards (and only forwards), the ground course should match the heading.
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But when I try to fly autonomously, the drone turns to the direction of the black line abruptly which does not seem to change its heading or allign with the nose of the pixhawk, which is a huge hindrance in conducting a flight. The black line seems to be acting as the direction of the nose, even when it is moving forward.
Now we are getting there. I still do not understand your problem, but we are getting closer.
Can you post your mission, or a video of it?