The winning values of k are the numbers in {1,...,1000} that are coprime with 1001, i.e., not divisible by 7, 11 or 13.
Despite the repetitions in Bibi's collection B for brevity we call it a set in the solution and denote the number of its elements by ∣B∣. The allowed operation is choosing a k-element subset of B and increasing each of its elements by 1 modulo 1001.
Let us show that a winning number k is coprime with 1001. Assume on the contrary that gcd(k,1001)=d>1 and consider any set B chosen by Bibi. Let the elements of B have sum S. Suppose Alex chooses k numbers from B of which m are 1000. Then the operation increases S by (k−m)−1000m=k−1001m, a number divisible by d in view of gcd(k,1001)=d. Hence the operation does not change S modulo d, for any choice of B. Let B contain one number 1 and ∣B∣−1 zeros. Then S≡1(modd) persists after each operation, while the desired "all zeros" final state requires S≡0(modd). The contradiction proves that gcd(k,1001)=1 is a necessary condition for k to be winning.
Conversely, gcd(k,1001)=1 is sufficient. For a proof consider the unique integer l in {1,...,1000} such that kl≡1(mod1001). Let B any set chosen by Bibi and b∈B an arbitrary element. It is enough to show that there is a sequence of operations that adds 1 modulo 1001 to b without affecting the remaining numbers in B.
Take a (k+1)-element subset C of B that contains b. This is possible as ∣B∣>k. Apply the operation l times to each k-element subset of C. Each element of C is contained in exactly k such subsets, so the procedure increases it kl times modulo 1001. Because kl≡1(mod1001), the result is that each element of C is increased by 1 modulo 1001. Now take the k-element subset C∖{b} of C and apply the operation 1000 times. After all described operations each element of C∖{b} is increased by 1+1000=1001 modulo 1001 with respect to its initial state, meaning that the operations do not change it. Clearly the elements of B∖C do not change either. The only change concerns b which is increased by 1 modulo 1001, as needed. Hence gcd(k,1001)=1 is a sufficient condition, and the solution is complete.