I also think you’re in the right place… it’s stored in the registry, under the name of the event log. I have a custom event log, under which are multiple event sources.
HKLM\System\CurrentControlSet\Services\Eventlog\LOGNAME\LOGSOURCE1
HKLM\System\CurrentControlSet\Services\Eventlog\LOGNAME\LOGSOURCE2
Those sources have an EventMessageFile key, which is REG_EXPAND_SZ and points to:
C:\Windows\Microsoft.NET\Framework\v2.0.50727\EventLogMessages.dll
I think if you delete the Key that is the log source, LOGSOURCE1 in my example, that should be all that’s needed.
For what it’s worth, I tried it through .NET and that’s what it did. However, it does look like each custom event log also has a source of the same name. If you have a custom log, that could affect your ability to clear it. You’d have to delete the log outright, perhaps. Further, if your app has an installer, I can see that the application name also may be registered as a source in the application event log. One more place to clear.