Is there an existing or a way to create a shortcut that will call a specific batch script to run to avoid opening manually those dialog boxes and clicking ok multiple times?
You might be able to implement something else that can do the same thing. If you provide the details of exactly what your current batch process does, we might be able to suggest alternatives.
This batch process changes PDF properties (author, title etc).
That can be done with various PDF libraries as a standalone application,
unrelated to Acrobat.