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Now clarify as to whether this is copying from db2 to mysql only or if you have to synchronize the two, i.e if you have to copy from mysql to db2 as well.
you have other functional questions to ask as well like
Can there be duplicates and are you supposed to detect them?
Are you allowed to extend the original tables with extra columns to mark them as processed?
Personally I don't see the point of JMS here (it's best for integration between two Java systems and all you're doing here is DB work). I would also not use an application server for batch processing involving huge data, especially since you are already using spring which offers spring batch. Maybe with the container you'll gain with some transactional aspects if you can XA and only commit if you have both written to target and updated source as processed.