@arcanus,
This will not solve the problem with your unit, but it is the solution I use to protect valuable data. I install a drive in another PC that is capable of housing all the data on the NAS box. (I currently have 2x1 TB drives in the NAS in a RAID 1 config, and a 1 TB drive in a PC down the hallway in another room). When I add anything to the NAS I always add it to the backup drive first, then let an FTP utility copy it to the NAS box twice daily on a schedule. I also make sure that the PC with the backup drive is on a separate UPS or surge bar, preferably on a different wall outlet and the outlet is on a different breaker in the house. Then I am relatively assured that I will have a good backup in case something happens to the NAS itself, or if a surge takes out an older breaker, or anything of that nature. I also burn a disc with the important bits on it weekly. I know this is not an absolutely ideal way to protect valuable data, I am working on using this same system but having the NAS in a good friend's house in a different province than I'm living in.
I know it does sound like overkill, but I do have some very valuable data that I absolutely cannot afford to lose. And although having the NAS is good, in case 1 of the drives fail, it is really not enough protection. If the NAS itself does something nasty to 1 drive, it will probably do it to both. Or, if a power spike hits the UPS with the NAS attached and somehow makes it past the surge protection, it will probably take out the whole NAS too. Having a NAS only insures that you are protected against a drive failure, and very little else.
So, when it comes time to update my firmware, first I make a disc of the important data, I then flash the NAS and reset it to factory defaults. And then, if necessary as it has been in the past, format both drives in the NAS itself. Then I copy all the data back off the storage drive in the PC that holds it.
Then if I ever encounter a problem like you are having, the likelihood of losing anything very important, or thousands of hours worth of work, is maybe 1%. And once I have a NAS in a friend's house about 1500 miles from my location, it is virtually zero.
Just my thoughts about your problem and a solution to making your data loss almost impossible. Hope it helps you in some small way.
Ryder