Word for an object that undergoes a removal?

The thing from which something is subtracted is the minuend:-

The quantity from which another quantity, the subtrahend, is to be subtracted. In the equation 50 - 16 = 34, the minuend is 50. [American Heritage Dictionary]

As explained in the above definition, the thing subtracted is the subtrahend:-

A quantity or number to be subtracted from another. [American Heritage Dictionary]

So you could say the duplicates were removed from the minuend.

OK, it sounds like we're focusing on lists of words. In that case, people in IT often talk about "populating" things, so we might say that something from which words have been removed has been depopulated - though I don't know if that's a standard term.

But I think you said you're looking for a noun. If that's the case, then I'm stuck at the moment, unless master list, original list or default list would work.

There are a number of words, but they tend to have connotations attached to specific contexts. There is remainder:

I smashed the country and western CDs in the music collection, but I still listen to the remainder.

In the law, the remainder is what's left of your estate after creditors and the tax man get through with it. In mathematics, it's what's left over after long division, as in "when you divide 11 by 7, the remainder is 4."

You could use remnant, if you don't mind the connotation of the left-over portion being small. The same with residue, which has its use as a term of art in chemistry to designate what's left over after a chemical reaction. Residue also has a definition in the mathematical field of complex analysis.

The word imported from Latin, residuum, is a more general term, and the OED finds uses of the residual as a noun meaning the "product of a residuum.