I tried parsing through all your details, but I'm going to ask a couple more questions.
What is the status of your RAID 5 array that you were presenting out as a datastore in VMWare? Is it healthy or is it presenting an individual member disk up to ESXi?
With things not working correctly, I'd reboot the host and get into the controller to find out the status of that array. I wonder if the array is degraded or some settings on the controller were lost (you DID say you had dead/bad batteries)...hence why the RAID 5 array is no longer being presented as a whole, up to ESXi.