Manchester City are preparing a British-record package worth around £130m for Fernandez, who wants the move before Tuesday's deadline and was absent once more as Chelsea beat Brighton.
Alonso didn't dress up his reasoning.
"We'll see. We want the best for the team and that's why we made the decision against Luton and today and anything that happens before Tuesday evening, we need to be aware of what is going to develop," he said.
"We are not sure, we are preparing for all the scenarios but I am sure that whatever happens from Wednesday we will have a good enough squad to compete in all the Premier League games."
Chelsea are lining up reinforcements of their own regardless of how the Fernandez situation resolves, with Monaco's Lamine Camara among the names linked, and the Argentine's exit is expected to go through provided the fee is right and a replacement is in place.
Pedro Neto's situation is murkier. The Portugal winger, deployed as a wing-back this season, has attracted interest from Liverpool among others, and Alonso stopped short of ruling out a departure even after a bright display against Brighton.
"No, in football I don't guarantee anything, not anyone. But I was very happy with Pedro. He did really well, he played with a lot of energy," Alonso said. "He is going to be very important for the team for the whole season because he has different special qualities.
"He is a threat in one-v-one, he attacks very well in the space, he is strong, he is competitive. I am happy that he scored, he was really close to scoring another one. I am very happy with Pedro."
The mixed messaging - genuine praise alongside a refusal to commit - leaves Neto's future almost as unresolved as Fernandez's, even if the Argentine's exit now looks by far the more advanced of the two situations.