what does reformat mean referring to an academic paper?

According to www.answers.com, "reformat" (in computer science) means to change the arrangement of data in a storage device.

So in using that term for academic writing/academic papers, my guess is that you'd be changing it from one format to another ... perhaps from APA format to MLA format.

http://owl.english.purdue.edu/owl/resource/560/01/
http://owl.english.purdue.edu/owl/resource/557/01/