Consolidate All Footage not working

After Effects refuses to consolidate duplicate assets that share an identical file path.

In Premiere Pro, I use the "Replace with After Effects Composition" command to send clips to a new project. This process automatically places the media at the root level of the After Effects Project Panel. At the end of the project, I need the assets in After Effects to match the organization I have in Windows Explorer so I manually import my Footage and Images folders from my hard drive into the project.
 

This results in two versions of lots of different files. One version is the asset sent from Premiere Pro at the root level, and the second version is the one nested within my imported folder structure. Both versions point to the exact same file path on my disk and share identical interpretation settings. When I run the Consolidate All Footage command, After Effects fails to recognize them as duplicates and nothing is removed.

How do I get this to work? I can’t have a messy project at the end and I don’t want to have to keep track of this stuff as I’m working.