Node types from CND file refresh fail

When modify custom node types in CND file which loaded at repository initialize,
throws exception:

ERROR jcr.RepositoryNodeTypeManager - Node types were read from the system content, and appear to be inconsistent or invalid: Test Repository
Message: Supertype 'jj:name' from type 'jj:content' does not exist

Investigate method refreshFromSystem of RepositoryNodeTypeManager, it will also refresh the custom content type from the CND files, but the refresh do not maintain the dependencies of node type.