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I understand your problem as you "want to change parameter while nodes are running", am I right?

Hopefully so, then does $ rosrun dynamic_reconfigure dynparam list return the node you want? If not, that node is not publishing dynamic_reconfigure-able parameters, which is the root cause of the problem you're seeing. Since rqt_reconfigure uses dynamic_reconfigure API internally, it can't see what dynamic_reconfigure can't.