I think the key mistake here was allowing the complexity of his higher-level filesystem arrangements (raid, etc) to leak into his lower-level backup routine. M

I think the key mistake here was allowing the complexity of his higher-level filesystem arrangements (raid, etc) to leak into his lower-level backup routine. Making a system backup like this should just be about imaging the raw disks, regardless of OS, filesystem, raid arrangement, etc. sda is sda is sda, period. Keep it simple and you drastically reduce the likelihood of making a mistake like this. A copy of Knoppix and dd will do the job just fine. Paragon Software, Clonezilla, ntfs-3g, mdadm -- distractions. Even better, if you keep the fundamental units of your system simple (a raw image of sda), you maximize tool compatibility / availability and your chances of recovering when things aren't going to plan.