FAQ: The PDF source document has permissions already set. Does this affect Safeguard PDF Security?

No.  If a permissions password has been set then Safeguard Writer ignores any existing permissions.

Document Open Password

If you have a document open password set then you must enter this in order to protect the PDF file.  This password will be removed by Safeguard PDF Security when the document is protected because it adds no additional value to the security of the protected PDF document.