The quickest way to get this back up and running is to go grab the item.dbf from a day or so ago (e.g. folder 20070905), paste it into the NEWDATA folder (it will want to overwrite what is there, say YES), and then refresh the system.
If you want to keep your menu changes that you already made, you could theoretically back up the ITM.DBF that's in the NEWDATA before overwriting it with the one from a day or two ago. However, I would just put the old one back for now and do the changes over again. Obviously, something is wrong with this one (it's corrupt or it's missing an item), and it can be a pain to track down.
This is more of an "old school" Aloha problem that we used to see a lot. If an item is attached to a submenu, and you delete that item, this would be the result (along with a pannicked phone call from a customer). However, I thought the newer versions like yours preventing you from doing this. Did you make these changes with through Excel or something?
A little tip: After you make changes, run the Verify utility under the Utilities. It's helpful for catching errors like this, and even smaller ones like forgetting to assing a Tax ID or putting someting into sales category. Even us old timers who have been working with Aloha forever still forget these once in a while too.
Friendly advice: It sounds like your trying to take the place of dealer for this restaurant. Nothing wrong with that, but I would keep their number handy if you're going to be learning as you go. Nothing will send a restaurant (and you) into a panic like when the system is totally down and you get it up and running quickly.
Tek-tips is a great place to ask questions, but not the best place for getting fast replies in a situation like this.