Manual obstacle avoidance (aka Stick Mixing)

I’m an experienced Arduplane user, but not so much with Copter and looking for a bit of advice. I’m planning a low altitude copter survey below the height of a couple tall smoke stacks. I see no way to safely flight plan around them. I will use FPV to spot them coming, and if needed I will take evasive action. In Plane, I simply use Stick Mixing to alter the course, then when I let go the plane resumes the programmed flight path. Copter doesn’t have this option, so what method is best? I could switch to LOITER Mode to navigate around the obstacle, but then when I switch back to AUTO, the copter will not resume the original flight path (observed in SITL). Instead, the copter will make a new path by proceeding direct to the WP. This will mess up my whole flight line and give me inadequate sidelap on one side.

Has anyone found a good method of dealing with this issue.