You can't remove a countably infinite number of elements one element at a time. Consider the following family of sets: $A_0 = N$ and $A_{i+1} = A_i - \{i\}$. The empty set can't be a member of this family. Assume $A_{z+1} = \{\}$. Then $A_z = \{z\}$ and $z$ is the largest natural number. I don't see how assuming $A_0$ is uncountable would change anything.
Edit in response to comments.
Tomasz is correct this can be proven using arbitrary intersection. Show there is a collection of sets such that every element of S is missing from some set in the collection. The intersection of this collection will be the empty set. What you can not do is "remove single elements recursively".
The intersection of a collection of sets is a single operation. This is why $\cap_{k<\omega} A_k = \{\}$. Recursively taking the intersection of two sets at a time will never give us the empty set.
$(A_0 \cap A_1) = A_1$
$(A_0 \cap A_1) \cap A_2) = (A_1 \cap A_2) = A_2$
...
$\cap_{k \leq n} A_k = A_n$
Induction does not help either. We can easily prove $\forall A_x \exists y(y \in A_x))$ using induction. The basic problem is the empty set is a finite set. We can never get a finite set by removing one element from an infinite set.