Custom Counter Data is cleaned up after the data has exceeded the Keep Period. It is also possible to delete the custom counters individually. This does not disable the custom counter in the agent configuration group. If new counter data is received from the Agent, the counter is recreated.
In PerformanceGuard go to Administration > Agent Configuration> Custom Counter Clean and you should be able to see all of your Custom Counters.
You can delete a Custom Counters by clicking on the button that appears to the right of the Counter you wish to delete, when you hover over it.