The SAMPLELINE flag in histogram was set during the BKE_histogram_update_sample_line function. That function in turn is called during every scope update in area draw function, meaning that during render it constantly gets set. OTOH the operator tries to disable the flag on invoke, which "cancels" the sample line by default. So during render the operator un-setting of the flag has no effect, because the render job immediatly triggers a redraw, which updates scopes and sets it again. Moved the flag out of the actual sample line update function into the operator execute. Now only the operator enables/disables overall sample line drawing, while the rest of the update works as before.