Uniquate = Eliminate or replace duplicates, make unique?
Solution 1:
Your idea 'uniquate' is possible but few would understand its intention without a lot of context.
uniquify
is not an officially recognized term, but uses the very productive and understandable suffix '-ify' meaning 'to make'. However this particular construction sounds too informal as a neologisms to be appropriate.
A single term is not necessary. You can say what is happening:
remove duplicates
Solution 2:
How about disambiguate? Webster’s dictionary defines it to be:
to establish a single semantic or grammatical interpretation for.