my 2c
-Upgrade the FI: if you can, use "Infrasturcture auto install"
-reboot FI: I would not do that; just check your ESXi if multipathing / teaming is ok, meaning you see path a and b. Then disable all the uplinks from e.g. FI-b, which will automatically bring down all the vhba's / vnic's attached to fabric b.