To generalize this issue a bit: CC Mode is not intended to
be used as a reformatter for old code in some more or less
batch-like way. With the exception of some functions like
c-indent-region, it's only geared to be used
interactively to edit new code. There's currently no
intention to change this goal.
If you want to reformat old code, you're probably better off using some other tool instead, e.g. GNU indent, which has more powerful reformatting capabilities than CC Mode.
File mode specification error: (void-variable c-font-lock-keywords-3)
This is due to a bug in the function
eval-after-load in some versions of (X)Emacs. It
can manifest itself when there is a symbolic link in the path
of the directory which contains (X)Emacs. As a workaround,
put the following into your .emacs file, fairly early on:
(defun my-load-cc-fonts ()
(require "cc-fonts"))
(add-hook 'c-initialization-hook 'my-load-cc-fonts)