Only footage is linked when you create an After Effects project. Importing an AEP file just brings in the comps and the links to a project. Once imported the original composition has nothing to do with the current AE project or comp files. You may delete the original with no problems. It has always worked this way.
If, however, you have your original AE project and the footage associated with the project and you delete the original project and the original footage, the footage will be gone. The compositions will be there but all of the footage will be missing.
You can use the collect files feature to collect all of the footage and create a new project file for one or all of the comps in a project. This will copy the footage from it's original position to a new folder and create a new aep.
I hope this clears things up. Your assumption that deleting or changing an AEP imported into After Effects is not correct.
Wrong choice of words on my part as I meant to say what you just described. Thanks for your clarification. Nonetheless, I found the script that I mentioned if anyone else is interested. It's called rd_MergeProjects