Okay, I just figured something out. Hopefully I'm correct with my assumption: I used the project manager again to transfer the files and unchecked the "remane files to match project" box and when I opened the project just now the clips kept my renaming in the project window. This is interesting. So basically, it returned the files to their original names in the file structure and kept my names untouched in Premiere. So, it works well.
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