А это твой любимый race condition в официальной документации mysql:

Data loss is possible if redo log files and data files reside on different storage devices, and an unexpected exit occurs before data file writes are flushed from a device cache that is not battery-backed. If you use or intend to use different storage devices for redo log files and data files, and your data files reside on a device with a cache that is not battery-backed, use O_DIRECT instead.