Thanks for your input.
I won't use an array again, I'll just rsync the data in the future (which I'm planning to do to a remote Pi-based OMV anyways). As said, luckily I do have a backup which is only one, maybe two weeks old and thinking about it I will probably only lose cell phone pictures of that timespan - in the original format, I have a backup of those in reduced size via Google.
So I'll just stop here. Thank you all for all your help, although we couldn't fix the problem - I'll just live with it.
And always remember kids, have a backup of your backup - otherwise I wouldn't yet come to that decision.