VMFS Datastore upgrade from version 5 to 6 if those datastores are set as boot from SAN Datastore:

i am planning to upgrade the vmfs of version of the datastore which have esxi boot partition on that datastore. i have a vcenter in which all the ESXi are set to boot from the SAN and ESXi boot partition are stored on the separate ESXi Datastore. We have updated version of the datastores except these. What will be the best practice to upgrade the VMFS?