What kind of production systems are you upgrading? I have a Linux box that I upgraded from 5.005 to 5.6 and I lost nothing. In fact, I had to manually delete 5.005 from my system just so I would make sure that I didn't have any old 5.005 modules lying around mucking things up.

Of course, it's always a good idea to just go ahead and reinstall the modules that you need anyway. Many modules contain code that may have been updated since the last time you used them or contain code that doesn't work quite right in 5.6. If you've used CPAN, you should have a log that keeps track of which modules you have installed. You can use that log to update your system.

Another good reason to use CPAN.