A bit impossible to give a good answer without knowing more about the problem, like why B needs to update the database, why it matters that the message arrives too fast etc... your probably the best one here to answer the question.
From the information you have given the only suggestion I can give is to let 'Y' tell 'B' about the file or let 'B' ask 'Y' about the file when it recieved the message.
if you can easily detect if the file transfer is completed (because file size is in the JMS message or because you can scan the file), then you can just throw an EJBException if it is not complete
another approach would be to write a JCA connector that basically wait until the transfer is complete (you don't really need any JCA funtionality, but the rules for EJB's does not apply to JCA connectors so it is an easy way to workaround those EJB restrictions)
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