If I had to guess, and this is a guess. The USB drive is disconnecting before the machine reboots. ESXi installs in multiple ways depending on what you install it to when it comes to a host. If you install to a volume smaller that 5GB or to USB storage it installs as embedded and runs ESXi in memory. If you install it to a hard drive with a capacity of more than 5GB then it actually runs from the hard drive instead. My guess is that your USB drive is becoming disconnected at some point and ESXi is continuing to run or there is a problem with the USB drive or port in some way. We experience this when we install on SD cards and the SD card or adapter fail while the host is on. The host sees the disconnect but continues to function. When it reboots, it loses every change since last boot. Go to the console of the host and hit alt+f12 to look at the live log and look for errors on the USB HBA.
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Next time run backup.sh before you reboot and then check the timestamp of state.tgz to verify if the script really had worked.