so it looks like this is what needs to be done. However, I know you're not supposed to run chkdsk on RAID
Not sure who told you this but it's absolutely INCORRECT. chkdsk has to do with filesystem, not RAID / hardware. The OS MUST be able to check the file system health which means running chkdsk.
RAID just means performance, but chkdsk doesn't impact performance, if it does your RAID isn't very good. chkdsk should not interfere, but chkdsk MUST be able to run for the OS to work properly, otherwise you can't fix problems.