Canford Cliffs is set to try and avenge his Sussex Stakes defeat by Frankel in the Queen Elizabeth II Stakes on Champions Day at Ascot on 15 October.
The five-time Group One race winner, who won the Sussex 12 months ago, was beaten by five lengths on Wednesday.
"We will run a few tests, but that was defintely not the Canford Cliffs we know," said trainer Richard Hannon.
"Had we been beaten a couple of lengths I could have accepted it. Hopefully we will get another crack at Ascot."
Frankel was called the "best horse I've ever seen, with Blushing Groom and Shergar" by his trainer Henry Cecil after making it eight wins from eight races with victory in the Sussex at Glorious Goodwood.
Canford Cliffs followed favourite Frankel closely but fell away in the final furlong.
"The first thing that [jockey] Richard Hughes said when he got off was 'he is not himself'," Hannon added on his website.
"He claimed that he was off the bridle before halfway, and Canford Cliffs has never been off the bridle in his life.
"He went to Goodwood in top order - his blood was good and he scoped well too, and, while Henry (Cecil) might be right in saying that Frankel is the best horse that we have seen, I would have expected to have been able to stay with him longer.
"He has won five Group Ones, so we know that he is a very good horse, but it was worrying to see him hang so badly left in the final furlong," added Hannon.
"He did it both in the Greenham at Newbury and the Prix Morny at Deauville last year, but it is the first time that he has gone walkabout this season.
"I know he won the Sussex last year, but I still maintain that Goodwood is not his course.
"He prefers the likes of The Curragh or Ascot, where the ground comes back at him at the finish and Ascot would be the obvious target."