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At first I thought the question was ambiguous: it's not clear whether you want the minimum number of moves or the expected number of moves. But a few experiments (with N < 1001 marbles and bowls) showed that the number of moves was always the same...
Suppose there are N marbles and N bowls, where N is odd. Let f(j) be the number of times bowl number j is chosen in some sequence of moves. Then the change in the number of balls in bowl j is f(j-1) + f(j+1) - 2 f(j) (where the j+1 and j-1 are taken mod N). If bowl #0 is the one that starts with N marbles, we want f(j-1) + f(j+1) - 2 f(j) = 1 for 1<=j<=N-1. Writing this as f(j+1) - f(j) = 1 + f(j) - f(j-1), we see that f(j+1) - f(j) = a + j for some constant a, and then f(j) = j^2/2 + (a-1/2) j + f(0). In order to have f(N) = f(0), we need a = (1-N)/2, and then f(j) = (j-N/2)^2/2 - N^2/8+ f(0). The minimum value is at j=(N-1)/2: f((N-1)/2) = f(0) - (N^2-1)/8. Since f(j) can't be negative, we need f(0) >= (N^2-1)/8. Then the total number of moves is sum_{j=0}^{N-1} f(j) = f(0) N - N^3/12 + N/12 >= (N^3 - N)/24.
Now it seems that f((N-1)/2) must be 0, so that the total number of moves is exactly (N^3-N)/24. This means that it is impossible to get more than one ball to bowl number (N-1)/2.
Consider a minimal sequence of moves that ends with two balls in bowl M = (N-1)/2 or M+1. Without loss of generality we may assume it is M. It's convenient here to regard the bowls as numbered -M to M. Let f(j) be the number of moves where bowl j is chosen, and x(j) the final number of balls in bowl j. Note that S(i) = sum_{j=i}^M (j-i) x(j) = f(i) for i >= 0 (this sum started at 0, stayed the same on any move except from i or -M, increased by 1 on every move from j, and there were no moves from -M), while for i < 0 the sum started at -Ni so f(i) = S(i)+Ni. Let k+1 be the lowest-numbered bowl (of -M to M) that balls were taken from. Of course k <= -1. The last move was taking balls from M-1 to M and M-2, so x(M-2) >= 1. By minimality, the last move from bowl j (for k+1 <= j < M-2) came before the last move from bowl j+1, so the ball moved from j+1 to j in that last move is still there, i.e. x(j) >= 1 for k <= j <= M-1. So f(k) = Nk + S(i) >= Nk + sum_{j=k+1}^{M-2} (j-k) + 2(M-k) = (N+2k)^2/8 + 7/8 >= 1 contradicting the assumption that balls were never taken from bowl k.
This is still not completely satisfying because I don't have a proof that the process will ever end (as indeed it doesn't if N is even). But if it does, the number of moves is (N^3-N)/24 = 41791750.
Department of Mathematics
http://www.math.ubc.ca/~israel University of British Columbia Vancouver, BC, Canada V6T 1Z2