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Argentina midfielder Fernandez has been linked with the Premier League club throughout the January transfer window after catching the eye at Qatar 2022.
Benfica coach Schmidt was frustrated by Chelsea's attempts to sign Fernandez earlier in the window when it was claimed they did not intend to pay his £105million (€120m) release clause.
Schmidt, who dropped Fernandez for one match, said the Blues were trying to "drive the player crazy" as it appeared he was keen to make the move.
Yet it was suggested on Monday a bid had been lodged that would see Chelsea match the £105m clause, giving Benfica no option but to allow their prized asset to leave.
The Portuguese giant is top of the Primeira Liga and through to a last-16 Champions League tie against Club Brugge, and Schmidt believes they are set for their next move if Fernandez departs ahead of Wednesday's (AEDT) transfer deadline.
"I think we always have to prepare everything in the background, especially at the end of the transfer window, and especially when you are not in the driver's seat," Schmidt said.
"So, we all know that we have a situation with Enzo that he has a clause in the contract. That means if the player wants and there's a club that pays this amount of money, you cannot stop that.
"Of course, for this moment, you have to be prepared and you have to find solutions. But at the moment, he is our player, he's still there, so there is no deal.
"We will see what happens in the next two days. Then I'm happy when the transfer window is closed and we can focus completely on our players in the squad and we can try to play a top season."
Despite removing Fernandez from the team at the start of the month, Schmidt has no concerns around the player's mentality now.
"Of course, he gets our full support," the coach added. "He's a great person and a great player, and I think I said everything about that topic.
"I already said a few times that as long as the transfer window is open, you always have to expect that something can happen. It's the same with the Enzo topic.
"So, we will see what happens in the next two days. But my mindset hasn't changed in the last weeks. I really appreciate after the discussions at the beginning of January that he was able to focus again on Benfica.
"I think he played top games for Benfica, which shows what I said before – that his attitude towards Benfica is 100 per cent.
"But we know also how the football business is. I think I'm always very honest, as honest as possible, to you here in the press conference. That's the situation. I cannot say anything more about this topic."