Continual instruction tuning enables large language models (LLMs) to learn incrementally while retaining past knowledge, whereas existing methods primarily focus on how to retain old knowledge rather than on selecting which new knowledge to learn. In domain-specific contexts, maintaining data quality and managing system constraints remain key challenges. To address these issues, we propose an automated continual instruction tuning framework that dynamically filters incoming data, which identify and reduce redundant data across successive updates. Our approach utilizes a small proxy model for efficient perplexity-based filtering, and updates the proxy to ensure that the filtering criteria remain aligned with the evolving state of the deployed model. Compared to existing static data selection methods, our framework can effectively handle incrementally acquired data and shifting distributions. Additionally, it addresses practical deployment challenges by enabling seamless model updates, supporting version rollback and incorporating automatic checkpoint evaluation. We evaluated the system in real-world medical scenarios. It reduced computational costs by 66.7% and improved model performance, and achieved autonomous updates, thus demonstrating its effectiveness for automatic continual instruction tuning.