Question

Puppet How can i remove all the node entries that are no longer managed by puppet

Answer 1

You could try this:

class remove_unmanaged {
  # always test with noop first!
  resources { 'host':
    purge => true,
    noop  => true,
  }
  # remove ALL unmanaged host resources
  resources { 'host': purge => true }
}

This would ensure that all unmanaged entries are removed.