Imo you're method of copying your current files to a third drive, checking manually, then copying to the existing backup seems sound. Although personally, I'd probably just keep the files on your backup drive as-is unless they are out of date/being worked on, and copy
those files to a 3rd drive.
I'm not sure what OS you are on, but it's worth checking the S.M.A.R.T status of your drives (most drives have some form of smart unless they're really old) to see if it flags any errors. For windows I'd recommend doing an error-check by right clicking on the drive in My Computer -> Tools -> Error-check, and also use something like SpeedFan (
Download SpeedFan - Access temperature sensor in your computer) to check S.M.A.R.T status. If you're on OS X I can't remember exactly what options you will have available to check drives but I imagine there are things under 'Disk Utilities'. Of course none of that really helps if the drive is failing already - but it dosn't hurt to check your other drives.
If this is all commercial work I'd also recommend having an off-site backup, doesn't matter what it is, just something that isn't linked to your main computer. Even if you have a backup on a second drive that's in the PC, if that gets a power surge for example, or anything major happens to your computer/home/office, you will lose it all because it's in the same place. Perhaps routinley backup on to a 3rd device and take it somewhere off-site, portable hard-disk/sd cards/whatever and put it somewhere else away from your computer. You could also use a web based backup but that depends on how much data you have/want to backup, and it might be costly.
You mentioned RAID drives - well, theres no such thing really as a RAID 'drive' (well there are probably some sort of RAID devices but they will have more than one drive in them), a RAID is more than one disc setup to act 'as-one'. There are many options for a RAID, and I
think it's done mostly on a hardware level/through your motherboard.
RAID - Wikipedia, the free encyclopedia
The simplest raid setup's are, for example, using two or more discs together acting as one whole drive - can increase performance as the computer can use both drives at the same time to get the complete data, but if one drive fails, you lose everything. A simple backup option is having two drives that mirror each other, they have the exact same data written to them at the same time, so if one fails, theres an exact copy on the other. There are loads of options for this so you're best bet is just google something like 'raid backup options' and your OS.
As Anvh mentioned, it could also just be your program/os that's messing up, or it could just be those couple of files acting up. If you think the drives failing though, just get rid of it, not worth the risk to be honest.