Latimeria,
I'll need more information to help work this out.
From what you wrote, you have a matrix of 12 X 17 = 204 entries representing consumption percentages, some of which are zero. And I assume that by a "fixed value of diet breadth" you mean that for each predator, the sum of the amounts of all its prey stays constant. But I would need details on how values are to be re-arranged. I'm guessing that you mean for example, if predator A has five prey items, totaling 100%, then you want to randomly select new percentages for those same prey items, again totaling 100%. Also, I'm not clear on what is meant by "dietary similarities" and how those are measured.
I'd suggest that you first write down a list of steps, in words, in great detail as to how to perform the computation you want to do, including the math calculations needed for any step that needs them. This would constitute a description of a procedure as to how you would do the entire bootstrap process by hand. You can post that description here, or if you prefer, email it to me. From there, it could be rewritten as a program in Statistics101.
John