I suspect that the data was lost because of file system corruption, combined with a file system check/repair on on of the boot attempts.
That's just a partial answer, since the cause of the (theorized) file system corruption isn't completely clear. If the failing disk somehow had bad data (that could still be read without an error), then that could do it. If somewhere along the line you had to pull the plug to power down the NAS, then that could create corruption too.
If you accidentally pulled/reinserted a different disk (say disk 1), then that could explain it also.
