If you're going to keep the same regimen I'd reformat those drives, every time, before a backup is written to them. This will let the drive update its bad block list. Stop and go is hard on a drive; don't do it . And, not to get into a holy war, but I've rarely had issues with Linux's ext{2 and 3} filesystems, and I've never had issues with BSD's {UFS1 and UFS2} filesystems. You can do better than Windows. If you're managing that much important data you shouldn't be running it on consumer grade crap, no matter what it costs you. False savings. Real data protection is a lot more complicated than getting another 2TB drive from Big Comp Storefront.

Good luck and post your progress (maybe in the lounge; this *is* APUG )