Leaving Cooper out of a 38-man training squad for the Rugby Championship - one that features 11 rookies and no Brumbies as they prepare for their quarter-final against the Hurricanes - is a clear sign Cheika has lost patience with the flighty Kiwi-born Queensland playmaker.
Don't expect Cheika to close the door entirely, such are his limited options, but two years out from the next World Cup seems a good time to make intentions clear.
Cheika has initially preferred Bernard Foley and Kurtley Beale as the Wallabies first five-eighths. Beale last played for the Wallabies at the 2015 World Cup.
Unless injury strikes, Cooper will remain on the outer. At 29 and after 70 tests, his future looks bleak.
Ahead of the first Bledisloe Cup showdown in Sydney, Cheika can't afford to be worrying about one of his backline directors becoming a sideshow against the All Blacks yet again.
He's got enough on his plate, as it is.
Attempting to pull together a Wallabies team from the five Australian franchises that haven't managed a win against their Kiwi Super Rugby counterparts since May last year (0-30 record) is plenty to consume his time.
Unfortunately for Cooper, test rugby requires a first-five that can be relied upon to deliver certain traits. No doubt he has talent, creativity and flair, but Cooper appears to have lost confidence, temperament and the ability to control a match.
He can't be trusted to deliver a game-plan under pressure; to not make crucial mistakes.
And his track record suggests his emotions get the better of him on the big stage.
Against the Highlanders in Dunedin last week, Cooper did little to inspire.
One of his cross-field kicks went sailing out on the full and he still needs to be protected on defence by being stationed on the wing.
In this regard, he is a liability. Shaping your defence around one weak link at international level is simply madness.
Whether it is Aaron Smith's box kicks or any of the All Blacks power wings with ball in hand, one way or anther, Cooper would be exposed.
Since guiding the Reds to the 2011 title, a time when Will Genia's speed and running game made him the world's premier halfback, Cooper has battled to recapture his swagger. He now looks frustrated.
The reality is the last few years have produced minimal on-field highlights and far too many distractions off it.
There was his "toxic" feud with Robbie Deans, an angry outburst on social media from Argentina and the unsuccessful stint in France, where he quit halfway through a two-year deal at Toulon.
All this, after attacks on Richie McCaw in the lead-up to the 2011 World Cup, a tournament where he failed to fire and endured the wrath of the New Zealand rugby public.
If only fleetingly, Ewen McKenzie has been the only coach to get the best out of Cooper.
Injuries haven't helped, but his return to the Reds hasn't gone well either. Much more was expected.
Cooper remains capable of throwing the odd miracle ball. but two weeks ago, when the Reds knocked off the Brumbies, he gifted the visitors a try by losing the ball over the line, and then set up and kicked the match-winning penalty.
These yo-yo performances do not cut it.
Eleven Reds have been named in Cheika's extended squad - many of them young talents.
Such faith, it seems, no longer extends to Cooper.
