Automated strategies are always persisted on a chart whenever it is open, even if Enabled is set to false inside the chart Strategies window. For example, if you shut down NinjaTrader with an enabled strategy in a chart then reopen NinjaTrader, the strategy will still be applied to the chart with the property Enabled being set to false. This allows you to enable the strategy without having to reconfigure the parameters. When the chart containing the automated strategy is closed though, the strategy will not be persisted (stopped and removed).
An automated strategy can be reloaded by right mouse clicking in the chart and selecting the menu item Reload NinjaScript. Reloading of an automated strategy will remove the old instance of the strategy and add a new one in the chart.