Update: I finally discovered what this was. After much discussion with the Storage Team, I found that the LUN in question was only presented on one controller - that had subsequently failed, hence why the LUN dissapeared on host reboot.
Trawling through the logs, I was able to use information from them and the vSphere Web Client to piece together enough information for the Storage Team to recreate the LUN on the other controller and then present it to ESXi.