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FSDB operates on lower level and it is requires exclusive access to those directories/files, so it is not really ACL issue, but design of the DB. To backup you either need to stop FlowStorage service so it unlocks those files or ommit FSDB folder from you backup definition and use FSDB builtin backup.
Thanks, I reconfigured my backup to ignore files/directories it cannot read. That will backup everything until yesterday, which is good enough for me.