When I set up our online ordering, we broke up our menu in to two categories, Food and Coffee. 

Problem is, there is also an Item category that has posted some of our items twice.  If I delete those particular items on the site, it will delete them on our register.  may be a stupid question, but how can I delete this "category"  Thought maybe I could do it in the category section, but "items" isn't listed as a category.  

If I go in to the item section to try and delete the item, it wants to delete the item across our entire system. 

I'm not going to start taking orders until I can get this resolves, because I don't want it to confuse our customers. 

Thanks