To reason about and enforce security in dynamic software systems, automated analysis and verification approaches are required. However, such approaches often encounter scalability issues, particularly when employed for runtime analysis, which is necessary in software systems with dynamically changing architectures, such as self-adaptive systems. In this work, we propose an automated formal approach for security analysis of component-based systems with dynamic architectures. This approach leverages formal abstraction and incremental analysis techniques to reduce the complexity of runtime analysis. We have implemented and evaluated our approach against ZNN, a widely known self-adaptive system exemplar. Our experimental results demonstrate the effectiveness of our approach in addressing scalability issues.