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As Japan, I just took all 3 provinces from Communist China, but the warscore is only 50%. So I can't annex or puppetize. I started from a save as CChina to double-check, and indeed the country has no provinces. What the heck? What am I supposed to do?
This question / problem has been solved by JJAC4image
Are you sure they don't own another province with Victory Points somewhere else?
A country can be annexed only when it has 0 victory points (can be checked in the ledger) and doesn't control its capital anymore.
Moreover, only the country that controls the capital can annex them (and if it's the AI, sometimes it waits 1 or 2 days before annexing).
Post edited June 29, 2016 by JJAC4
As I said, I logged in as CChina and looked in the statistics page and they have no provinces listed at all.
Oops, I lied.

There was an option to annex in the main diplomacy list. Not inside of the sue for peace where I expected it. They gave the three provinces to puppet China, and I was still at war with Sinkiang.