Migrating existing groups from Commons 2.x to Commons 3
Commons maintainer japerry is in a team that created 
Commons Migration module exactly for your task.

Posted by nateswart on March 18, 2013 at 9:46pm
Provide a migration path from Commons 2.x to 3.x

It uses Migrate with Drupal-to-Drupal data migration to get the job done. Sadly, it's still in early development, and according to this feature request not quite finished yet. But at the very least you can see in code what approach original developers use.