Hey Innovative,
How exactly is this affecting your billing? Do you mean that it's causing confusion for your staff as they're unsure which items to select?
Am I correct to assume that this came up sometime after you performed a Verify and Rebuild on your QuickBooks file. I've seen strange scenarios with item duplication/ListID's changing after a QuickBooks Verify and Rebuild. However, I'm not sure if this is what actually happened in your case. Do you have any Item conflicts that show up on your Resolve Conflicts screen?
Since there aren't any prices associated with the duplicate items and you don't use them, then you should just delete them. Go to Customize > Screens > search for and View the Item List screen > then delete the items you don't need.
Let me know if you require further assistance.
- Ashur