updating parts of an ontology

[Bahador(reza)? OFOGHI]

Hi,
 
I have a super ontology that includes some sub-ontologies with a subClassOf 
relationship between a node of the super ontology and the root of the 
sub-ontology in each case.
 
My question is: if I want to update a sub-ontology, can I remove() the root of 
that sub-ontology from the super ontology and just add the new version again? 
Will a call of remove() actually remove the whole sub-ontology from the main 
super ontology or just that root node of the sub-ontology?
 
thanks,
BO