**Do NOT delete the item, as that will cause you to lose any previous rental history**
First, you'll want to edit the item with an indicator such as "DO NOT RENT" or "DO NOT USE", so that it is clear it is not to be added to future projects. Next, you'll then adjust the quantity of that item to "0", but ensure that you still have "Track Quantity" enabled. This will ensure that a conflict appears should the item ever be added to a project.
You've now made it clear this item should not be added to an order, and you've kept the history of this item in your account.