There are a couple different ways to handle that, but Acrobat isn't the best tool for that job. One option is a free file-naming utility called A.F. 5. Just Google it and download. It has been around forever and works great. Another option would be the functionality built into the (currently) free EDD Toolbar add-on for Excel, developed by Nikolai Pozdniakov. I believe you need Excel 2007 or 2010 to use it. It's also possible to address the issue manually via Excel based on the log file that is optionally created during the bates numbering stage, but that would take more explanation that I can get into here.
Hope that helps!
Jason Covey
PDF Litigation Solutions, LLC
www.pdflitigationguide.com