Problems with cluster re-size

I used Hard Disk Manager 11 to attempt to resize the NTFS clusters on 12.7TB RAID array. The system is running Windows 7 x64 SP1. I need to resize the clusters from the default of 4KB to at least 8KB, but I was attempting to go to 32KB so I don't have to do this again if I have to resize the array again. (What prompted this is I increased the capacity of the RAID array to 20TB and 4KB clusters allows for a maximum of 16TB.) Anyway, HDM requested a restart to perform the operation during the Windows preboot and it began working. After a period of time, the progress indicator made it about 2/3 of the way across. I know this operation would take a while so I let it run for days. After about 3 days, the system rebooted on its own. However, it appears the operation failed and corrupted almost everything on the partition in the process. The partition is still accessible from Windows but its contents are corrupted. (The partition is used for stored large quantities of media files.) I'm afraid to run chkdsk before checking to see if that will do more damage. Is it possible to try the operation again to see if it will run to completion? Any help would be greatly appreciated. (I don't have a backup because I can rerip my collection if necessary, it will just take a really, really long time.)