If you’re going to delete entries from enumerations, it’s generally better to rearrange them in such a manner that the unwanted entries are moved to the end of the list. The engine will then automatically apply the necessary changes (like in switch case nodes using the enum) wherever the enum is being used. Not doing so & deleting entries from mid way can sometimes cause the engine to keep looking for the old list as you mentioned.
What you could do in this situation is to either retry the deletion process from a backup copy after first rearranging the enum entries, or search and find every instance of the said enum & make sure it’s wired to the right nodes. If you won’t lose a lot of work in the process, I would definitely suggest the first method. Also in either cases, always make sure to save it before making any changes elsewhere.