I had some time so I ran some tests, simulating a filament runout. On a single print, whenever I simulated filament running out, Octoprint would pause the print. I could then resume it, and it would pick up where it left off.
So, even though the message in the top taskbar is still there, each runout would pause the print. Success!!
I did alter the Octoprint GCODE scripts for resuming a print:
{% if pause_position.x is not none %}
; absolute XYZE
M82
G90
; reset E
G92 E{{ pause_position.e }}
; move back to pause position XY
G1 X{{ pause_position.x }} Y{{ pause_position.y }} F4500
; move back to pause position Z
G1 Z{{ pause_position.z }} F4500
; reset to feed rate before pause if available
{% if pause_position.f is not none %}G1 F{{ pause_position.f }}{% endif %}
; re enable filament runout detection
M412 S1
M83
{% endif %}
Would be nice though to be able to clear the message in Octoprint.