Is it safe to "FLUSH STATUS" in mysql?
Is it safe to execute Flush status in production ?



Well it should not affect anything as such but resets the status counters and you should be "Safe".



  Is it possible to reset Max_used_connections alone ?



No



  but "We need to find out Max_used_connection after deploying ...."



How about introducing graphs into monitoring? Say Cacti / Grafana will give you good glances over what's-going-on-inside-your-mysql!