The hive [HKEY_CURRENT_USER] is subset of [HKEY_USERS\S-1-5-xxxx] that details out the profile of the current user;
The hive [HKEY_CURRENT_CONFIG] is a subset of [HKEY_LOCAL_MACHINE\Config] that details the current configuration;
The hive [HKEY_CLASSES_ROOT] is combination of [HKEY_LOCAL_MACHINE\Software\Classes] and [HKEY_CURRENT_USER\Software\Classes] with class definitions.
Registry Healer scans only one hive of these doubled keys. All corrections applied to only one set will be reflected to another set too.
To avoid deleting of registry entries that are necessary for some programs Registry Healer has several excluded lists. These excluded lists contain registry entries that should not be deleted or changed. Other registry cleaners may not have that and will find and remove important registry keys.
Also, Registry Healer has the excluded drives list. Into this list user can add drive letters of paths to ignore when scanning the registry. For example, if you do not want to remove registry references to files on a CD-ROM that currently is not in a drive or on a removable drive then you can add their drive letters into the this excluded list. Many registry cleaners do not have the such list and look for all references to all drives. And while scanning you may see the "Please insert a disk into drive X: (Abort, Retry, Ignore)" message.