This is, more or less, working as designed. The semantics of transient are precisely that the data is not persisted. The entity returned from entityManager.merge(obj)
is, in fact, an entirely new entity that maintains the state of the object passed into merge (state, in this context, being anything that is not part of the persistent object). This is detailed in the JPA spec. Note: There may be JPA implementations that do maintain the transient field after the object is merged (simply because they return the same object), but this behavior is not guaranteed by the spec.
There are essentially two things you can do:
Decide to persist the transient field. It doesn't really seem to be transient if you need it after merging the class into the persistence context.
Maintain the value of the transient field outside of the persistent object. If this is what meets your needs, you may want to rethink the structure of your domain class; if this field is not part of the state of the domain object it really shouldn't be there.
One final thing: the main use case I've found for transient fields on domain classes is to demarcate derived fields, i.e., fields that can be recalculated based on the persistent fields of the class.