When password-protected PDF files are being imported from the Hot Folder, the files go to the Exceptions folder unprocessed as the password wasn't entered.
But, if you import your password-protected PDF file into the scanning station, there is a graphical interface to enter the password:
You can also setup the Import from Hot Folder option in the Scanning station and point it to the folder containing all password-protected PDF files.
That way you can import all password-protected PDF files by clicking the Scan Pages button.
Another workaround is using an XML-ticket. You can find an example via the link: XML-ticket examples for FineReader Server 14.