Stokes, the Test vice-captain, is currently suspended by the England & Wales Cricket Board while he is the subject of an ongoing police investigation following his alleged involvement in a late-night brawl in Bristol in early September.
The 26-year-old was left grounded when the rest of England’s squad flew out to Australia last weekend and although the ECB have been reluctant to rule him out of the Ashes completely, Bayliss knows the chances of Stokes facing Steve Smith’s men is remote.
Even if the police do not charge Stokes, he still faces an internal ECB disciplinary probe that will only start once the criminal investigation has been concluded.
Asked if he had written Stokes off for the Ashes, which begins in Brisbane in three weeks’ time, Bayliss said: “I have. If he turns up it’s an absolute bonus.”
With his playing future in limbo, Bayliss admits he has no idea when Stokes will be available again.
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“Haven’t got a clue,” he said. “It’s totally out of our hands. We have just got on with preparing as best we can.
“The players have a very important, tough series coming up and they are totally focussed on winning it. They are concentrating on playing without him. We can’t worry about something we can’t control.
“If any team lose one of their better players it’s going to be upsetting to a certain degree. But we have time to smooth things out and find the right combination. We certainly wouldn’t be here if we didn’t think we could win without him.”
The focus on Stokes threatens to undermine England’s preparations for the Ashes, which start with a two-day tour match against a Western Australian XI at the WACA in Perth on Saturday.
Bayliss, though, is confident his players can deal with the increased scrutiny a tour of Australia brings and the inevitable questions over their missing talisman.
“It’s something you’d much rather not have to deal with, but that’s life,” said Bayliss. “It’s happened, and we will have to answer those questions and get on with it.
“The Australian media will hammer away and try to put the pressure on in other areas as well. We have to try to deal with that and keep it separate from what we are doing on the field.”
Even without Stokes, though, Bayliss is confident England can still get the better of Australia.
“We certainly wouldn’t be here if we didn’t think we could win without him,” he said.
“Certainly, we’ve been playing some good cricket, so have Australia. But they are beatable.”