I like the opposite -- save the original as 'config.orig' or 'config.old', or perhaps 'config.2006-07-21' for example. Then, save the new one as 'config'. It's pretty common, and it gives me a point of reference when I go to customize the new one.
What's really best, though, is when a package recognizes an obsolete config file and saves a 'config.old', a 'config.defaults', and a 'config' that has all the options from 'config.old' updated to match the new format and adds any settings from 'config.defaults' that used to be hardcoded and now aren't. Preferably, the new config file will be set up with things specified as much like the old version worked even if the default behaviors have changed, and with notes in the config file's comments stating what's changed and why. I can't name a CPAN module that does this currently, but I've used a few server and desktop applications that do this. That's one of the biggest things I like about the CMS I recommend for my clients, actually. When they upgrade it (or hopefully when they pay me to upgrade it), the upgrade is almost seamless.
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