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Assuming that you set the Audit logging level of a service like the Batch Report Service to "Basic".
When you disable this service in Cognos Configuration start Cognos, and re-enble the service again and restart Cognos, you'll notice that the Audit logging level is reset to default (Minimal).
This is because when the service is being "disabled" in Cognos Configuration, then re-enabled, all the settings are reset to default.
This is not a defect and it works as design. In fact, when the service is disabled, it is de-registered in Content Manager. This means that all the settings for that service are removed. When the service is re-enabled, it is once again registered in Content Manager, and all the settings are reset to default. This includes the logging level.