This is going to be NP-hard! I believe you can do a reduction from Subset Sum to this.
As per BlueRaja/polygene's comments, I will try to provide a full reduction from Subset Sum.
Here is a reduction:
Subset Sum problem: Given integers x1, x2, ..., xn, is there some non-empty subset which sums to zero?
Our problem: Given two integer arrays of size k, find the minimum possible difference of the sum of the two arrays, assuming we can shuffle around the integers in the arrays, treating both arrays as one array.
Say we had a polynomial time algo for our problem.
Say now you are given integers T = {x1,x2, ...,xn} (multiset)
Let Si = x1 + x2 + ...+ xn + xi.
Let Ti = {x1, x2, ..., xi-1, xi+1, ..., xn } ( = T - xi)
Define
Ai = Array formed using Ti
Bi = [Si, 0, ..., 0] (i.e one element is Si and rest are zeroes).
Let mi = the min difference found by our problem for arrays Ai and Bi
(we run our problem n times).
Claim: Some non-empty subset of T sums to zero if and only if, there is some i, for which mi = 0.
Proof: (wlog) say x1 + x2 + .. + xk = 0
Then
A = [xk+1, ..., xn, 0, ...0]
B = [x2, x3, ..., xk, S1, 0, ..0]
gives the minimum difference m1 to be |x2 + .. + xk + (x1 + ... + xn) + x1 - (xk+1 + .. + xn)| = |2(x1+ x2 + .. xk)| = 0.
Similarly the if part can be proved.
In fact, this actually also follows (more easily) from Partition too: just create new array with all zeroes.
Hoepfully I haven't made any mistakes.