According to [ODO](https://en.oxforddictionaries.com/definition/deduplicate), there is a predictable answer:

> **deduplicate** [verb] [with object]
> 
> Eliminate duplicate or redundant information from (something,
> especially computer data)
> 
> ‘they can deduplicate files uploaded by many different users to keep
> costs lower than otherwise possible’

A [Google Ngram](https://books.google.com/ngrams/graph?content=deduplicate&year_start=1800&year_end=2000&corpus=15&smoothing=3&share=&direct_url=t1%3B%2Cdeduplicate%3B%2Cc0) shows that it is used (if not all that often). Apparently in bursts.