I downloaded the 5.12.3 installer to upgrade my 5.12.1 installation. After installing 5.12.3, my previously installed cpan modules are gone. Is this expected behavior? Should I be backing up my library before upgrading to prevent this?
It is expected behavior. Next time you can use "autobundle" feature of CPAN client, it will create list/bundle of modules to reinstall using CPAN client in new version.