This topic on the QNAP forum provides multiple cases of the NAS failing after either a reboot, or a firmware upgrade. Some users hint to the firmware problem of some kind, but generally the descriptions are as follows
TS-409 lost configuration after reboot
I have a TS-409 (2.1.0 Build 0904T firmware) with 2x WD10EACS drives in RAID1. Following a reboot the device has dropped is showing as an unconfigured device. The drives are showing as ‘Invalid’…
I think that [updating firmware] may have caused this.
I have encountered similar problem with TS-409 QNAP version 2.1.0 (0624T) with 4 1 TB Seagate drives in RAID 5 configuration. All my settings are lost and the message says the server is not configured yet.
And then there is another topic on a similar, if not the same, issue
Suddenly TS-219P reports “Hard Drive Missing”, “Install and format at least one hard drive before using the NAS…”
Yesterday we installed an upgrade of the system software and added a user…
We don’t have any Linux computers, only Windows.
First of all, the basic sysadmin rule is if it is not broken, do not fix it. Once the NAS unit is assembled, configured, and filled with data, there is little, if any, need for firmware upgrades. Firmware upgrade in a NAS often involves rewrite of the entire operating system inside and migration of old settings to their corresponding last version equivalents. This does not always go smooth, so they warn you every time you’d better have backup before updating firmware.
If your unit has automatic firmware update, turn it off once you complete the initial setup.
However, once things start crashing around, we can still recover data with our Home NAS Recovery. Firmware update does not usually go around trashing actual file content on the disks. The configuration is lost, but this is something our software can handle.