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There is no general answer, because this need to be checked for every application. A change in the ptSetConfig→ulSystemFlags can Many indications can be seen as informations for the application and only a response is necessary.
But some indications need deeper implentation. For example if the application change the stack behavior with ptSetConfig→ulSystemFlags, than it make is necessay to implement indications.
One example for that is the PNS DeviceName/IP Example.
A other example is the PNS Signal LED Example. If the device developer forgets to bring the signal LED on the case of the device or he want to use an other LED as Signal LED, is possible
to use the signal indication.