The impacts of clones on software maintenance is a long-lived debate on whether clones are beneficial or not. Some researchers argue that clones lead to additional changes during the maintenance phase and thus increase the overall maintenance effort. Moreover, they note that inconsistent changes to clones may introduce faults during evolution. On the other hand, other researchers argue that cloned code exhibits more stability than non-cloned code. Studies resulting in such contradictory outcomes may be a consequence of using different methodologies, using different clone detection tools, defining different impact assessment metrics, and evaluating different subject systems. In order to understand the conflicting results from the studies, we plan to conduct a comprehensive empirical study using a common framework incorporating nine existing methods that yielded mostly contradictory findings. Our research strategy involves implementing each of these methods using four clone detection tools and evaluating the methods on more than fifteen subject systems of different languages and of a diverse nature. We believe that our study will help eliminate tool and study biases to resolve conflicts regarding the impacts of clones on software maintenance.