Solution:
In general, Bob can find the values of all n integers asking only ⌊log2n⌋+1 queries.
For each of Alice's numbers xi, let Qi be the set of queries S such that i∈S. Notice that all Qi must be nonempty and distinct. If there exists an empty Qi, Bob has asked no queries that include xi and has no information about its value. If there exist i,j,i=j such that Qi=Qj, xi and xj could be interchanged without the answer to any query changing, so there does not exist a unique sequence of numbers described by the answers to Bob's queries (Alice can make her numbers distinct).
From the above, ⌊log2n⌋+1 is a lower bound on the number of queries, because the number of distinct nonempty subsets of {1,…,n} is 2n−1.
If Bob asks any set of queries such that all Qi are nonempty and disjoint, he can uniquely determine Alice's numbers. In particular, since the values x1,…,x2021 are relatively prime, each prime factor of xi occurs in the answer to query Sj iff j∈Q(i) (and that prime factor will occur in each answer exactly to the power with which it appears in the factorization of xi). Since all Q(i) are unique, all xi can therefore be uniquely recovered by computing the product of the prime powers that occur exactly in the answers to queries Q(i).
It is possible for Bob to ask ⌊log2n⌋+1 queries so that each i is contained in a unique nonempty subset of them. One possible construction is to include the index i in the jth query iff the 2i−1-value bit is set in the binary representation of j. So the answer is ⌊log22021⌋+1=11.