The 26-year-old did not travel with the rest of his teammates Down Under ahead of this winter's Ashes, having been suspended while an investigation into a night-time brawl continues.
Bayliss admits that potentially being without Stokes is a major blow for England, but he hopes that others in his ranks can step up to the plate for the five-Test showdown, which begins in Brisbane on November 23.
"Not having someone like Ben in the team will be a loss," he told Sky Sports News. "Any team that loses one of their better players is not going to be quite the team they may have been.
"We have just gone about things as we normally have. A good player can have an injury and you would be without them anyway, so we have just prepared with the guys that we have got here. There hasn't been any chat about him being here or not being here.
"We have just got on with what we have been doing. We are losing one of the leaders of the team in everything. Batting, bowling, obviously in the field, his contribution to the team off the field, and he is a leader out on the ground as well. Someone else is going to have to step up."
England step up their preparations for their opening clash with the Baggy Greens by taking on Western Australia in a warm-up match on Saturday.