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Is acrobat reader pro provide scripting feature to run and add password to PDFs file via scripting (cmd , bat) ?
It is only possible when you create a plugin for Adobe Acrobat.
Actually, this can be done if all the passwords are the same.
It can also be done from a script by using a security policy that sets a password. Policies can be applied to a PDF with a script.
There's no such thing as "acrobat reader pro". You either have Acrobat Pro or Acrobat Reader.
The former has batch editing capabilities (although not if the files are secured with a password). The latter does not.