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New optical technologies offer the ability to reconfigure network topologies dynamically, rather than setting them once and for all. This is true in both optical wide area networks (optical WANs) and in datacenters, despite the many differences between these two settings. Because of these new technologies, there has been a surge of both practical and theoretical research on algorithms to take advantage of them. In particular, Jia et al. [INFOCOM '17] designed online scheduling algorithms for dynamically reconfigurable topologies for both the makespan and sum of completion times objectives. In this paper, we work in the same setting but study an objective that is more meaningful in an online setting: the sum of flow times. The flow time of a job is the total amount of time that it spends in the system, which may be considerably smaller than its completion time if it is released late. We provide competitive algorithms for the online setting with speed augmentation, and also give a lower bound proving that speed augmentation is in fact necessary. As a side effect of our techniques, we also improve and generalize the results of Jia et al. on completion times by giving an $O(1)$-competitive algorithm for arbitrary sizes and release times even when nodes have different degree bounds, and moreover allow for the weighted sum of completion times (or flow times).