We upgraded from 6.0 to 6.2, from 6.2 to 6.4 , and now 6.4 to 6.4.4
In every upgrade we found that some OOTB groups can get deprecated. or some new groups might show up.
A general practice which we follow for upgrade is...
1. Custom groups created by your team should be packaged and have merge or merge preserve mode.
2. Package your group and keep a backup.
3. Install this package post upgrade.