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A topic doesn't hold anything. What does is the node that publishes that topic. Either the node has a functionality to clear/unpublish a topic or you simply kill the node that has been publishing so far.

In your case amcl probably uses the map_server. As you want to run gmapping afterwards, you can just bring that down, i.e. kill the map_server, and probably also amcl. If you start gmapping then, no other map messages should be flying around.