Due to the fact that systemd-journal-flush.service has "Requires=systemd-journald.service", this service is stopped too when journald is requested to do so. However stopping systemd-journal-flush.service implies that journald relinquishes /var hence implicitly switching back to the volatile storage mode and removing /run/systemd/journal/flushed. If journald is started afterwards, it will run in volatile storage mode regardless of the value of 'Storage=' as it believes now that /var is not yet ready (because the flushed flag is missing). Because this flag is mainly an indication for journald that the initialization of /var/log/journal (during the boot process) has been done, systemd-journal-flush.service shouldn't be tied to the state of journald itself but to the state of /var/log/journal, hence to the state of the system.
System and Service Manager
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