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Each answer from the MQ Command Server is one message. So for example, to display 300 queues, the ReplyQ that the runmqsc tool uses (AMQ.5F728DF62BF23AFF in your example) would have 300 messages placed on it as a result of the command displaying all the queues.
If you have a lot of running (or stopped) channel instances (you suggest 12000 in your second post), in answer to a DISPLAY CHSTATUS command, then that would result in a lot of response messages.
The reply queue used by runmqsc is created from the model queue SYSTEM.MQSC.REPLY.QUEUE which, by default has a MAXDEPTH of only 3000. It would be perfectly appropriate to increase the MAXDEPTH of the model to a number big enough to allow the command server to place all the response messages onto the runmqsc ReplyQ. I suggest that this would be the simplest way to get all the responses back from the command server, and thus understand why you have so many channel instances.