Premiere Pro :: Change Original Source Files In Project?

I have a project which has become very disorganized over the last year of editing due to PPs poor ability to effectively share sequences/projects across multiple computers. My assistant editor used a different computer and so the links in the sequences point to multiple "source" files in the project (some in imported folders). However, there is ultimately only one original video clip. The problem is that Premiere Pro won't allow me to delete the nested versions of the source files without also REMOVING the clips in each of the sequences that uses them. For example, the project folder looks like this:
 
- Original File Folder
-- videoClip-001.mov
 
- Imported File Folder (imported on one of the many exchanges between editor and assistant editor)
-- videoClip-001.mov
 
- Sequence version 1 (Uses the second video clip, not the first - although they are ultimately the same video file)
 
If I delete the Imported File Folder, which only has a mirrored reference to the same video file as in the Original File Folder, then the clip in Sequence Version 1 dissapears. What I expect, rather, is to see a "missing media" message in the sequence so I can reconnect it to the version in the Original File Folder. But I can't. BIG HOLE in Premiere Pro CC.
 
Why do I want to do this? In a large project with hundreds of video clips, keeping order is very important. With the sequences using multiple "versions" of the same video clip, that order goes down the tubes and it becomes impossible to work.