I don't really follow what you're saying, but do you have the original video accessible in premier? If so, re-edit what ever you needed, and then import that back into after effects. If not, export the video from after effects to a video file which you can open with Premier and start all over again.
I have to restate part of that initial comment. I'm actselecting some footage from the timeline in Premiere, then right-clicking to create a composition in After Effects, when all of this happens. Does that make sense?
I'm not sure what you are trying to say. The behavior of Replace with AE composition is exactly that - it creates an AE comp as a placeholder in the timeline, where the original clips only exist in the comp, but on the Premiere timeline the container is visible? You cannot edit this comp any further in Premiere. If you need this functionality, you will have to use conventional nesting, duplicate timelines and sub-clips to virtually duplicate your footage, if the original edits need to be retained.
So, how would I go about using conventional nesting to duplicate timelines and sub-clips and would there ever be a reason for doing so? Maybe I need to rethink my workflow process?