Hales and Adil Rashid halted their first-class careers last month in favour of limited-overs contracts with their counties, in the belief it would allow them to improve in those formats both for the benefit of their international careers and also to make them more attractive to T20 leagues around the world.
Rashid remains a first-pick for both England's white-ball sides, but Hales has been sidelined throughout the one-day series in New Zealand following Ben Stokes' return, with Jonny Bairstow and Jason Roy given the opening roles.
Bayliss said that he did not have any involvement in the decisions made by Hales and Rashid, saying it was an individual choice, but he believed there could still be an overall benefit to maintaining a red-call career in order to further a players' limited-overs game.
"I said to him [Hales] when it came out, that not playing red-ball cricket, hopefully that doesn't affect him," Bayliss said. "If he plays red-ball cricket you get a quantity of balls, and that helps with any form of the game. He had to weigh that up with going away and having the extra time to work on his white-ball skills. Only time will tell. If it doesn't work, hopefully he is able to make a decision to come back into red-ball cricket."
Bayliss was aware of the possibility of Rashid making his career move from last year, but he was not at the heart of the players' discussions.
"Rash mightn't have said anything but he might have mentioned it in passing," Bayliss said. "We didn't have a long discussion about it if he did. I certainly can't remember it. But both those guys have their people they speak to at their counties and other coaches here. With Rash we knew it was a possibility from late last season. It's totally up to them."
Although both players indicated they may reassess their decisions after the 2019 World Cup, any realistic chance of resuming a Test career has likely gone. The door had previously not been closed despite Rashid being overlooked for Mason Crane in the Ashes and Hales not featuring since the end of the Pakistan series in 2016. In the last English season, Hales tried to reinvent himself in first-class cricket by moving into Nottinghamshire's middle and was briefly talked about as a potential option for the Ashes squad.
"From that point of view it is a big decision," Bayliss said. "Basically taking themselves out of the running for Test cricket. That might give us an idea of how they were personally thinking. We can't do any more - that's the decision they have to make and we have to move on."
Hales and Rashid will complete their current stint with England with the deciding ODI against New Zealand in Christchurch before the tour switches to Test mode. An important decision needs to made over the vice-captaincy following Stokes' return. Stokes officially remains the Test vice-captain, having had the role prior to the incident in Bristol last September; when he was forced to miss the Ashes it was handed to James Anderson.
Earlier in the tour, Test captain Joe Root said it was a matter that had still to be discussed and those conversations remain on the to-do list once the one-day series is concluded and tour moves to Hamilton for the warm-ups.
"To be honest, that hasn't been discussed as yet. I'm sure it'll be something Joe and I will speak about very shortly," Bayliss said. "[Stokes] was vice-captain because of his knowledge of the game and what he means to the team. But I thought Jimmy Anderson did a pretty good job during that Ashes series."
The next stage of Stokes' legal case takes place on Monday following his plea of not guilty to a charge of affray - with the first hearing at Crown Court which he was given permission to miss because of the ongoing tour.
Stokes has made a solid return to the international stage. He took the Player-of-the-Match award in Mount Maunganui, then battled against his natural instincts to score an important 39 off 73 balls on a tough pitch in Wellington, where he also took a super catch to spark New Zealand's collapse.
"We said before, there are always guys around the world who are able to put those things aside and get stuck back into it," Bayliss said, "and I think we have seen over these games that he has put it aside and got on with it."
In terms of the reception he has received, New Zealand has offered Stokes a soft landing back into the England fold - a boisterous crowd in Dunedin as lively as it has got - but while it has made managing the situation easier, Bayliss believed he would have been able to cope in Australia.
"It's probably been a bit easier for him to sneak back in. With Ben, I don't think it would have made any difference, it might have encouraged him even more to do well."