Another problem with the CPAN installation process is it does not delete files only creates and updates. Deletes are not part of the normal install process.

Your reorganizing the files, may have end up conflicting with older files that still exist. So you should

• Deprecate the older modules, for example, make them loadable but not do anything or they blow up. OR,
• See if your new code can live with the older modules without conflicts. So you will need to have copies of the older files sitting in the lib directory seeing if a problem will occur.