Fellas! I feel your pain! I have spec’d out some tools to clear unused and select active, but they don’t yet exist. Good news is that leaving a bunch of section planes in your model doesn’t hurt anything, but being the perfectionist that I am I would prefer to clear them out.
When you click on a scene, the active section planes are orange. I would suggest creating a temporary layer called “don’t delete”, cycle through your scenes and add each orange section plane to that new layer. Once you are finished, turn off the layer and clear the left over section planes.
It’s a manual process but it should only take a few minutes, and likely won’t need to be done that often. Let me know if that helps!