Oops sorry for the late reply. Completely missed it.
Conceptually, there is a step on the index phase which processes all the "queries" and associated "clicked" URLs and factors that in to be used as part of relevancy. If the "clicked" URLs no longer match what resides in the next, this process no longer occurs and essentially, you have disabled "click tracking ranking" factors.
However, not all is lost. By having click tracking, you still benefit from having the analytics and being able to view this information in the Marketing Dashboard.
In regards to using some other key to remove duplicates, Funnelback only provides you with the APIs to orchestrate that yourself outside the product.
There isn't a feature which automatically removes duplicates based on some metadata, unfortunately.