Yes, moving the PERC 6 over is fine and will retain the RAID config. You should not be considering moving the PERC 6 VD to a PERC 5. Because the PERC 5 and 6 are both supported on the 2970, the fact that some have PERC 5's probably also means their firmware is older. I would strongly recommend updating the BIOS/ESM/BMC on the target 2970 so that the PERC 6 is supported. 
Here's the background: Stupidly, a former colleague setup a CRM system on what was meant to be an old development server that had long since been retired from frontline service but somehow between him and one of our developers, this became a "live" server with real data being added to a virtual machine (it's running a VSphere hypervisor) . Sure enough the PowerEdge 2970 in question has just died (all sorts of voltage regulator error codes for the CPU 1 side of things) and as you can probably guess, no backups since he created this a year ago. I had a look at it today and tried a couple of the suggestions I found on here associated with the error codes but without any luck, so I guess it's probably the mainboard itself. We do have a couple of other retired but still working (at least, still booting) 2970's in the server room that I might be able to cannibalise to get this one running again for long enough to copy the virtual machine off. However, they're not exactly the same spec. Processor wise and memory wise they're a match but the problem machine has a PERC6i controller with six disks (and I've no idea what the current configuration of those disks are other than a note I found that indicates 2 disks are used for the hypervisor and the other 4 disks are used for the virtual machines) and the other 2 PE2970's have a PERC5 and no disks at all. I'm pretty sure just simply moving the disks across would be a bad idea and possibly risk the data on them. Do you think swapping the PERC6i and the disks across to one of these spares would work? Would the PERC6 retain the disk configuration as setup on the original server when powered up in the "new" server? Alternatively, there's the option of swapping the mainboard across from one of the working servers, though I'm not sure if there will be any BIOS issues with it suddenly finding a different PERC controller attached to it. Any suggestions or pointers would be appreciated? As you can probably tell, I'm far from an engineer or server admin for that matter. Just need to get the thing up and running for long enough to clone the virtual machine onto something a little more suitable (and warrantied). Thanks in advance. 
PE2970 failure - move disks to another PE2970?