Your best option inside the Acrobat environment is to use an "Action" (i.e. a Batch Process). You'll find tutorials on this topic here on the site, as well as a library of "Actions" other people have created.
But if you want to do this from an external program, there is an ActiveX interface to Acrobat that is easily programable from Visual Basic or Apple Script. You'd need to write a custom program for opening and operating on all the files of interest.
You can also use an Acrobat command line option to open a PDF and load an FDF at the same time.
The important bit is that the FDF can contain a script, that then resets the form. But this technique only works one PDF at a time.
Except for batch processing (Actions), Acrobat is intended to be used on the desktop by a user who is manually working on one PDF at a time. Adobe does not generally like people using Acrobat in a server like way, in fact the license agreement says something to this affect. So, to this end, Acrobat does not generally include options for operating on entire folders of PDFs, and especially not from the command line.
The source for PDF Scripting Info pdfscripting.com
All About PDF Stamps in Acrobat and Paperless Workflows - THE BOOK !!
The Console Window (Video tutorial)
The Console Window(article)
Having trouble, Why Doesn't my Script Work