We effectivly have two departments using the licensing server. One department upgraded to 2013, the other did not. The department that did only purchased enough 2013 licenses to run on their machines.
The other department did not upgrade their liceses, so still need to access to their 2012 licenses.
From what I can tell, the old .lic file had both subscription license entries in it for both departments and we then used reservations to make sure each department only received their licenses.
if all the licenses are on a current subscription
is their any reason why you can't generate a 2014 license
but keep the products at the version they are at currently
also make sure you install this hotfix for civil 3d 2012: http://usa.autodesk.com/adsk/servlet/ps/dl/item?si