The discussion about this was brought up by
DC-41. After checking the behavior of other ORMs (notably Hibernate), already fetched associations should not be overridden by subsequent queries, just like with other persistent state of already fetched entities. This saves performance and can assure a better integrity of the object model in-memory.
Entities and their associations that are already in-memory should only be refreshed if this is done explicitly either through EntityManager#refresh($entity) or through using the Query::HINT_REFRESH query hint on any query.