As of today, the EU Council's public register of documents lets you find only nine (public) documents that use the term "Brexit".
The only document published after the referendum that uses the term is this agenda of the Customs Union Working Party (it makes sense, though, that it's on the agenda of this committee).
It seems like the Council is avoiding to use this term, or it only appears in non-public documents that cannot be found through the register. In the overall public communication, especially in and around the European Council, the term seems to have been used more frequently.
But since even the phrase "UK referendum" can hardly be found (13 hits as of today) in public Council documents, I wonder whether the Council has already been informed that Brexit might happen soon or whether they are using some creative terminology when they talk about Brexit.