Shishkin stunned onlookers at Ascot when refusing to start in the Nirvana Spa 1965 Chase, which went the way of Pic D'Orhy.
Nicky Henderson's top-class chaser was returning to action in the Grade Two contest, which only attracted four runners.
Nico de Boinville was partnering the gelding, who was the short-priced favourite, but at the tapes, he did not budge and the race went ahead without him.
In Shishkin's shock absence, the Paul Nicholls-trained Pic D'Orhy and Minella Drama shared the lead in the early stages as Straw Fan Jack followed, with the latter becoming the danger when Minella Drama faded.
Pic D'Orhy and Straw Fan Jack briefly locked horns, but Harry Coben's mount pulled away when asked for a 16-length success at 5/2.
Shishkin leaves Henderson scratching his head
"What can I say?" said a dejected Henderson, who will now desperately search for an opportunity before the King George at Kempton Park on Boxing Day.
"At the moment I can't think of all of the programme and the pity is there is a three-mile hurdle at Newbury on Friday and I would run him that, but it closed this morning. Did I know this would happen?
"I don't know why he did that today, it's one of those starts where you are going away from home (stables) and the odd horse will do it. My biggest concern would be the King George start would be exactly the same. How could I guarantee he wouldn't do the same thing again? But I can guarantee if I took him down to the two-mile start here he would fly up. He would be in the lead.
"The alternatives, I will have to look, and if there is an open handicap I wouldn't mind running him, but as you know the programme doesn't allow these horses to run very often. If only it closed tomorrow Newbury would be brilliant.
"I don't know where we can go and I have to find where there is an open handicap. I know there are no conditions races left and the Peterborough is too close (to the King George). I don't know what to do.
"He jumps off every day, every day, every day. He's a quirky character at times, but he will always jump off. He will never turn his head, never. He was in a mood today and he wasn't for moving. He would still be there now.
"I can't read his head and I don't have the whole programme book in my head, but I can tell you there are no conditions races left.
"My biggest concern though is, if this was ever to be repeated, then Kempton isn't the place to try it. That's my biggest worry. I could say sorry he doesn't need a prep, he will go have a racecourse gallop and he will be ready for Kempton, but that start at Kempton does worry me."
'Job done' for Cobden and co.
It was very much contrasting emotions for Cobden, although he felt the winner was not at his best.
"Me and Theo (Gillard, Minella Drama) saw him (Shishkin) plant at the start and the one thing you don't want to do is stop when you are on a planter, so me and Theo were not going to make it easy for Nico," said Cobden
"When you are riding in a £70,000 race you don't want the favourite to jump off do you. It's unfortunate for them because it would have made it a horse race if he had jumped up, but from my perspective I was happy to jump off without him.
"I was happy our horse got the job done today, but I don't think he was anywhere near his best and he's been a lot better than this in the past. But he's got the job done.
"I thought he would canter round and beat the other two on the bridle and not have a race. I was happy to get past Theo but when you have Straw Fan Jack alongside you, I would say there is a problem you know. I looked across and I wouldn't say he was going better than me, but he was there. There's loads of improvement in him."
Blueking crowned Coral Hurdle champ
Blueking D'Oroux demonstrated his class with a taking victory in the Coral Hurdle.
The four-year-old was sent off at 4/1 in a field of five, most of whom carried with them more experience and higher ratings than Paul Nicholls' runner.
Harry Cobden bided his time, only asking the winner to throw down a challenge over the second-last and finding him comfortably able to go on and take the Grade Two by a length from Strong Leader.
Boothill booked his ticket to the Clarence House Chase as he continued his Ascot love affair in the Jim Barry Hurst Park Handicap Chase.
Harry Fry's eight-year-old won the race off a mark of 140 last year - and having acquitted himself well in some hot novice events afterwards, defended his title off a 15lb higher mark having triumphed again over the course and distance on his return to action.
Sent off the 11/4 favourite there was still all to play for as Boothill and Jane Williams' Saint Segal approached the last locked together, but a fall for the 5/1 shot opened the door for Johnny Burke and his willing mount, who had enough in reserve to repel a late rally from 7/2 second-favourite Frere D'Armes.
He finished with half a length in hand, to the delight of his trainer who had suffered a narrow reversal with Whitehotchillifili in the previous contest, and although holding an entry for the Tingle Creek at Sandown on December 9, Fry suggested his winner will now return to his favourite playground for a shot at the two-mile Grade One on January 20.
Chianti Classico was the toast of Ascot having successfully continued his chasing education in the Royal Ascot Racing Club Novices' Limited Handicap Chase.
A winner of all but one of his outings as a novice hurdler, Kim Bailey's six-year-old made a successful transition to the larger obstacles at Chepstow last month.
However, he faced a tough task when sent off the 4/5 favourite for this three-runner assignment, having to concede over a stone in weight on the quickest ground he has encountered so far.
Although not at his slickest over his obstacles at points in the three-mile event, his class came to the fore when it mattered as he pulled three-quarters of a length clear of Scrum Diddly after the last.