This is what I would do —
Move the original AE project away from wherever you have it saved. Duplicate that project file, make all your changes, then either place the new project file with the same name back to the destination where Premiere is looking for it, or open Premiere and when it asks you to link all of the missing media, link it to the new project file. As long as all of your Comp names are the same, it should automatically link to all of your new work while keeping all of the edits you made while in Premiere.