Software Systems of Systems (SoS) are large-scale distributed component-based systems in which the individual components are elaborate and complex systems in their own right. Distinguishing characteristics are their short expected integration and deployment time, and the need to modify their architecture at runtime, while preserving the integrity of the system. Integration testing is a commonly used technique employed in the acceptance processes of software SoS. In this paper, we propose a scheme to test a complete SoS at every reconfiguration, re-exercising the test cases of every updated component. In practice, re-executing all the test cases, whenever a modification takes place in one of the components, would be very costly. This is the case, in particular, when the system has to keep running all the time. Our proposal, therefore, encompasses several methods to limit the amount of test cases to be executed. The basis of all these methods is to rely on as much information as possible extracted from previous runs of the test cases. We illustrate our findings with an example SoS coming from the maritime safety and security domain.