Autonomous drone with pixhawk + raspberry

Hello everyone,
I have a project where a hexacopter needs to fly from its home-point to point B and after to point C (two pre-defined waypoints).
However, I need to be able to update this waypoints’ list during flight - changing for example point C by point D when it is still going to point B.
Is it possible to do it with Pixhawk? If not, do you know any flight controller that would allow that?
Obs.1: It needs to be done “autonomously”. I planned to do this list update using a Raspberry Pi (or another microcontroller) using wires/jumpers between it and the flight controller.
Obs.2: I said “autonomously” because I still want to have a Remote Controller (RC) connection in case I want to cancel the mission and bring it back manually (with the RC).
Thanks in advance, guys!