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If two terms in an ontology have the same alternate label, it does suggest that they may be closely related or represent the same concept. However, it doesn't necessarily mean that they are exactly the same.
On the other hand it can create confusion so I would say it can happen but then we should include clear documentation (using rdfs:comment for instance) on the difference if this is not clear enough by the ontology structure and relationships.
This may be important for implementation.
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