how to save uploaded file in a custom user registration webform in D7?
I believe 46 is the File ID or FID in Drupal. You can load it via file_load() and re-save, move it or attach it to a user profile however you like.

Webform has already saved the file in the system somewhere. You can find out where by inspecting the $file object after $file = file_load(46); and doing a print_r or vardump on $file.