That sentence should probably make you think long and hard about your backup strategy. I hope you get to the bottom of what caused this (and let us know; it’s bizarre the files should be non-zero in size but empty; perhaps try viewing them with cat from the terminal) but even more I hope that it makes you realise you need a backup strategy suited to the value of your data. If it’s of any value to you, I posted about mine here and have since added monthly backups to Blu-ray.
The need for a backup strategy is independent of the software you use; none is guaranteed to be fail-proof under all imaginable circumstances.