But the issue was, this was happening even after we removed all instructions to delete data from the flash.
The device had most traces between controller and flash completely hidden as a precaution for hacking/snooping, making it extremely difficult to diagnose the issue as the issue completely vanished in a test harness when the flash was connected to controller outside the board.
The problem also happened exceedingly rarely -- we needed about 100 of these devices to run constantly a certain operation and it took us to wait for about a week until one of these devices died on average. But we had millions of them in the wild and we would get hundreds or thousands die on our customers every week.
It took half a year of debugging and tens of millions of dollars in losses.
We found that one of unrelated components on the board emitted too much noises. And a software change to speed up writes to the flash removed a special sequence of that preceded and followed every one word write to the flash. This special sequence protected the flash from accepting a random noise as a command. Usually, the command would be something harmful or meaningless. But sometimes it would be interpreted as a real command -- and one of these was a command to clear entire flash chip.