A possible explanation can be found on part 4 of this post:
> [...] if the checksum is not valid, there is a loop that clears out the flash [...] I suspect (but haven’t tried yet) that if the battery of the controller dies while it’s writing on the flash, at the next startup the checksum does not match and the DS4 gets totally messed up like this one.
That is, according to that theory, it was trying to write something to the flash (perhaps while pairing?), and part of the write failed because the battery died. On the next boot, it detected a wrong checksum, and erased everything.