you can do that ..i had somebody on my team accidentally delete a few zones so when he went to activate the config it told him he was about to remove zones that he really did not mean to delete. I manually recreated those zones and put them back in the active zone set and when i selected to activate the config ..it no longer showed those zones as being removed. The system never knew what was going on.
I'm facing the following:  I created 2 IVR zones connecting an HBA to SPA and SPB of a CX4 which is in a different VSAN, but when I want to activate the zoneset the differences show a list of zones which are going to be deleted when the activation is actually performed. I can't figure out why this happened and I'm stuck. I have 2 options: 1) Recreate the entire IVR zoneset and activate the new zoneset 2) Look which zones are to be deleted and add them, before activating the current IVR zoneset  What option would you prefer and why ? How do I continue without the attached servers loosing connectivity for a brief moment ?
IVR Zoning shows too many differences when activating the IVR zoneset