What you are looking for is called existence checking in EclipseLink, and can be configured using the @ExistenceChecking annotation as described here:
http://eclipse.org/eclipselink/documentation/2.4/jpa/extensions/a_existencechecking.htm
Try specifying @ExistenceChecking(ExistenceType.CHECK_CACHE) as while it states that check_cache is the default,this is for Native EclipseLink projects. JPA projects use a Check_Database as the default to conform to the JPA specification requiring that merge calls merge into data from the database if necessary. Using the check_cache will prevent EclipseLink from querying at all, so you can query yourself based on your own criteria. Existing objects will be required to be in the cache though, otherwise there is nothing to merge into, and EclipseLink will have to perform an insert.
Another option is to use a customizer to define the DoesExistQuery used for each class. This could allow you to override the checkEarlyReturn method to perform as needed to determine existence.
The above options still use the JPA merge and so still require getting the existing data to merge into - so it will still require selects for existing objects not in the cache. If all you are after is an update all type statement that will update the object or insert the object as is, without tracking only what has changed, you might try looking at native EclipseLink functionality, such as the UnitOfWork api. Using something like ((EntityManagerImpl)em.getDelegate()).getUnitOfWork().updateObject(entity) or use the UOW execute your own UpdateObjectQuery would avoid the selects for existing objects, at the loss of only sending changes.
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