The Easter Road club have already turned down two bids from Championship rivals Rangers for the Scotland U21 international.
Hibs, who lost 6-2 to Rangers in the first round of the Petrofac Training Cup last Saturday, have reiterated they will not allow the 23-year-old to join their main challengers for the title and would rather see the player run down his contract and leave for nothing next year.
However, Stubbs has insisted that he still has a good relationship with Allan and expects him to carry on working to the best of his ability.
“He is a professional footballer and he has worked very hard and we as a club have worked very hard to get Scott to the position that he is at now,” said the Englishman.
“To let all that go then it could take an awful long time for it to get back again and I don’t expect that.
“My relationship with Scotty is very good. I respect him, not just as a footballer, but as person. He’ll be getting advised to do things but we expect him to be in every morning, train, train properly and get on with his job.
“I know that will be difficult, I understand that. But people have to respect, and it is important to say that, the position of the football club.”
Former Everton and Celtic defender Stubbs said the fact Allan had handed in a transfer request had not changed the club’s position on the matter.
“There is no change whatsoever,” Stubbs said. “I understand Scott’s position, I understand players do hand in transfer requests but our position has been very clear from the outset.
“In our process our stance as a football club has been that Scott Allan is not for sale to Rangers and the transfer request doesn’t alter that one bit.”