As per the description above, you want to protect a PDF file without opening it, Is that correct?
Protecting a PDF file without opening is not possible with Acrobat. You can protect a PDF file with password after opening it. For detailed information refer to Protect PDF files with permissions | Link: https://helpx.adobe.com/in/acrobat/how-to/security-permissions-protect-pdf-files.html
Feel free to update this discussion for any further assistance.
You can use the Action Wizard to create a single action that will encrypt (protect) all files in a folder. You run it from Acrobat, so Acrobat has to be open, but the several files are automatically opened, protected, closed without having to individually open them.
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It can also be done using a stand-alone application, independently of Acrobat.