Thank you very much for your help.
I was expecting duplicates after the Mendeley import and merged them appropriately. My "Duplicates" filter was already at zero before discovering I had the disambiguated PDF duplicates in Google drive. Also the disambiguation varied from (1) to (8) for different files.
Today, I checked the Google Drive Webapp and was surprised that the duplicated PDFs no longer exist although what remains is the most recent disambiguated file (e.g. papername(8).pdf). I checked my Google Drive folder on my Mac and this is also the case. I'm not sure what caused this. I did do a Resync and Cleanup but I did not see any change after an hour or so, so I thought it did nothing. Maybe this is what got rid of the duplicates?
As for the duplicates appearing in my root folder, I just deleted those and it seemed to have no negative effect on my paper entries as they are still linked to the PDFs inside the Paperpile folder.
I'll use the support widget now but I thought I'd chime in here in case someone also had a similar problem.