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Container-based virtualization has become a promising deployment model for industrial applications mainly due to its benefits, such as providing support for co-located applications in heterogeneous environments. However, such facilitation brings challenges, including full temporal isolation among real-time applications and support for time-critical applications. In this paper, we tackle such challenges, in particular when the applications are time-sensitive Control Applications. The literature suggests that flexible timing constraints for Control Applications are beneficial in responding to disturbances and minimizing response deviation. Therefore, we propose a mechanism to support such a runtime adaptation in container-based virtualization. To show the performance of the proposed mechanism, we implement our approach on a Linux-based hierarchical scheduling platform, and we evaluate it for a Control application.