Removing options from select boxes on catalog items can cause problems
In the past people have asked How do I Remove an option from select box variable in the catalog item form? And you'd think it would be something as simple as a
active flag. However if you look there is no
active flag on select box options. That is truly unfortunate.
If you delete it, the values will still hold their
value but if there was a display for the value it won't show that.
There's really only one way I know of. Client script and remove the option until you can safely delete it.
The client script would be really small
Another way... that is really overkill but I think handles it the best, is to disable the item and make a new version of the item.