I have been contacted several times in the last couple of week about the removal of LUNS from an ESX host. In every case the Storage Admin had masked the LUN away from the ESX hosts on the storage array. This is NOT the way to do it. It will result in a APD (all paths down) to the LUN. A side effect will be that hostd will be affected and start disconnecting in vCenter.
When removing a LUN from an ESX 4.x host you will need to use the “esxcli” commands. kb 1015084
When removing from ESX 5 things have gotten a lot easier. Now you can do most from the vSphere Client. Check out the following kb 2004605
The give away here is: Never just remove a LUN from the SAN that the ESX host has access to. Even though you have removed all virtual machines and nothing is running on it. Before doing anything on the storage array, you will need to detach the LUN from the ESX host.