The champions lost Tiemoue Bakayoko to a groin problem sustained in the 3-3 Champions League draw with Roma on Wednesday, while N'Golo Kante is still sidelined with a hamstring injury and Danny Drinkwater is yet to make his debut due to a calf issue.
David Luiz was used as an auxiliary central midfielder against Roma and Conte admits similar tactical changes could be needed against Marco Silva's side.
"At the moment, I can say nothing about the starting XI," he told a news conference. "We have many doubts. I hope to try to recover some players in these 24 hours."
Asked if Fabregas is their only fit senior midfield player, he replied: "Yeah, that could be the case."
He added: "I'm not happy changing the role of my players. I think every player has his own role. But, sometimes, you have a situation where you have to adapt and you must be ready to pay for this. It's normal."
Conte says he is unwilling to rush Drinkwater into action too quickly but had a more positive update on Kante, with the France international now expected to return before the next international break at the beginning of November.
3 - This is the first time that a team managed by Antonio Conte has conceded three goals in a Champions League game. Shellshocked. pic.twitter.com/81rh5ygISc— OptaJoe (@OptaJoe) October 18, 2017
"Danny is progressing well. Now he has started to work. It's very important for him to progress well and improve his physical condition," he said.
"It's very important to recover him very well. If I try to put him on the pitch without good fitness, I risk another injury.
"I hope to have Kante back very soon, before the international break. He's progressing well, the scan was better. He's started to work, [but] not with the group.
"If he's available before the games against Roma and Manchester United, I would be very happy.
"Every year you build something and put something new into your team. That was my first season. Now, this season, we are trying to rebuild something at Chelsea. We lost a lot of big players, a lot of big players who wrote the history of this club. Now we're trying to rebuild.
"This season we changed five players, we bought five players. We are trying to rebuild something important. It's normal that you have to pay something in this situation."
Watford have lost just one of their last six league games and came from behind to beat Arsenal 2-1 in their last outing, and Conte expects a difficult test at Stamford Bridge.
"Watford are doing very well. They had a really good transfer market and strengthened the squad very well," he said.