The LLD documentation should explain what happens when the low level discovery tries to set up an item/graph but a regular item/graph with the same key/name already exists. From what I know it will not be created then.

This would be different from the behaviour of templates. Templates, when applied, "take over" existing non-templated items which then belong to the template and get deleted once the template is removed.

By the way - is there a reason for this difference?