Hi Andrew,
I don't know if the persistence provider (not the container) tries to help you, but theoretically speaking it should treat 2 instances of different classes completely independent. If on the other hand, you marked a field or a property as a @Version, the provider will check that the version of each entity didn't change in the course of the transaction, and will throw an exception if it did.
Now about the merge: it's not possible to merge values from 2 different entities. You can call em.refresh to refresh the version value, but then you'll need to reapply the changes to the instance again.
Regards,
-marina
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