According to ODO, 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 shows that it is used (if not all that often). Apparently in bursts.

According to ODO, 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 shows that it is used (if not all that often). Apparently in bursts, though it's possible that most of the examples in the earlier tranches (if not all) are typos and the like.