SmaugFUSS 1.6 already supports area files from SmaugFUSS 1.4, Smaug 1.4a, Smaug 1.02, and SmaugWiz (and maybe others too?). But if you ever edit anything about the file online, the first time you foldarea that area will be converted to SmaugFUSS 1.6's room resets instead of the previous area resets. We've provided Nick with the info that's been changed for SmaugFUSS 1.6, we just haven't heard back yet whether or not he plans on making Area Editor able to edit the new file format. Take a look at the other thread on this topic:
http://www.gammon.com.au/forum/bbshowpost.php?bbsubject_id=5323 to see what we'd provided earlier. As for making a program to convert older format Smaug files to SmaugFUSS 1.6's new format I don't do any of my coding in windows and wouldn't know where to begin on it, but if Nick needs to see what's been changed in SmaugFUSS 1.6 to get to the new reset system, Samson's snippet for it is readily available at http://www.smaugfuss.org/downloads.php?file=resetfix.zip for whoever'd like to undertake the project you've suggested or just to modify their own Smaug codebase to support this system instead or even to fix Area Editor. :)
[EDIT - 11 March 2008] - The Smaug FUSS site is now http://www.smaugmuds.org/