Programmatic filefield value/Default Filefield value
The new version of the file should be saved as a managed file. This will provide a file object that has a fid which in turn can be used by the file field.

Here are the docs for the function used to save a managed file.

https://api.drupal.org/api/drupal/includes%21file.inc/function/file_save_data/7

The value for a file field contains the following

fid - The fid property of the file object returned by file_save_data.

description - The description may be used as the label of the link to the file. 

display - Determines whether a file should be displayed when outputting field content.