EndNote 20 has an option called PDF handling (available from EndNote preferences). This enables the conversion of an existing folder of PDF files into new EndNote references by extracting Digital Object identifiers (DOI) from the PDF files. The associated PDF file will be attached to the newly created reference - see example below.

Where the DOI is not available a record with the PDF name will be created (no author/no title) see below. This record can then be edited with full details to create a complete reference.

To access these settings, go to the Edit menu, select Preferences, and then select PDF Handling from the list of preferences, select a PDF Auto Renaming Option (please be aware that there is a 50 character limit). Select the ‘Enable automatic importing’ check box to enable automatic importing of your PDFs. Select the folder from where you want EndNote to import your PDFs. Download or copy your PDF files to this folder for automatic importing and renaming.

After EndNote runs the import operation, EndNote creates a subfolder called Import within the Auto Import Folder. EndNote also imports a copy of each PDF to this folder.