One of our application is under upgrading process and it is in downtime. But when I go to dashboard and drill down to user action purepaths we are still seeing dynatrace capturing those and also there is a gradual increase in count of values in dashlets for timeframe. Is this possible? What am I missing here?
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Are you referring to a downtime as configured within AppMon or the actual application being down as part of the upgrade? The former only applies to incidents so that you don't get emails or create incidents during periods you know there are going to be outages and maintenance, the agents will continue to be capturing data.
You can think of these agents as being a part of the application process, so during something like an upgrade they should only be offline and not sending data for the time the application process is down as part of the upgrade. When everything is set up correctly as long as that particular application process is up the agent will be up and active regardless of if other processes or servers are down.