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:
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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.

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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.