When I first started, I added one folder (files were named rather miscellaneously) to Calibre and then had most damnable time trying to determine which pdf is which. So, if you have duplicates, it's probably faster to add them one by one. AFAIK, Calibre can't grab original filename into comments or custom column, it must be entered manually.
When you have small bunch of books in Calibre, check for duplicates, delete what you want and export renamed files to the new folder (which will eventually replace the folder where they reside now). If you noted down the original filename, you can easily find and delete them from the original location.
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