Yes, this is true. Suppose C∗ is such a chain complex of free abelian groups.
For each n, choose a splitting of the boundary map CntoBn−1, so that CncongZnoplusBn−1. (You can do this because Bn−1, as a subgroup of a free group, is free.) For all n, you then have a sub-chain-complex cdotsto0toBntoZnto0tocdots concentrated in degrees n and n+1, and C∗ is the direct sum of these chain complexes.
Given two such chain complexes C∗ and D∗, you get a direct sum decomposition of each, and so it suffices to show that any two complexes cdotsto0toRitoFito0tocdots, concentrated in degrees n and n+1, which are resolutions of the same module M are chain homotopy equivalent; but this is some variant of the fundamental theorem of homological algebra.
This is special to abelian groups and is false for modules over a general ring.
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