New illustrator file groups after "edit original" not appearing in AfterEffects

I imported an illustrator file into Aftereffects and then noticed I needed to make some adjustments (these adjustments were mainly putting shapes into new groups so that I could manupulate them in Aftereffects better.)

I have live update enabled in Aftereffects , so after I finished my adjustments I clicked save on the Illustrator file.

When I went back to Aftereffects, I saw that the shapes I placed into the new groups were gone completely, and only the old groups remained. I tried looking in the composition and the file layers in imported files column, but no luck. Reload footage seems to be disabled. 

Is there any way to fix this? I know a quick fix would be to re-import the scene, but I want to know for the future in case I'm deep into a project and have to do this without reseting the transforms and layering done within Aftereffects.