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There could be multiple reasons.
for eg, Agent is not sending the data to the controller and could be a problem with agent or agent is sending the data but controller not displaying it due to various reasons.
Can you please let us know that if you are able to see BTs, snapshots etc and the problem is only with application flowmap. Please share controller logs under /Controller/logs folder and one of the agent logs with us. Also, please share screenshot depicting an issue to assist you on this.