I guess you are asking about proper cleanup after LUN is "unpresented" from host on either fabric or the array.
The host reboot should definitely clean this up.
If you can't reboot then check this post from Cormac Hogan: Best Practice: How to correctly remove a LUN from an ESX host - VMware vSphere Blog - VMware Blogs
It should give you an idea and some hints on how to clean up properly.
Hope this helps.