There is definitely no counterexample for convex polyhedra and no counterexample for bodies with smooth boundary with non-degenerate second fundamental form. (In the latter case even small open subsets of the boundary cannot be deformed, the argument can be found e.g. in Spivak volume 5.)
I do not know if the question was asked somewhere in full generality, although it sounds very natural.
If one could prove a sort of stability estimate: if the intrinsic metrics of surfaces are $\epsilon$-close, then the bodies are $\delta$-close, where $\delta$ depends on $\epsilon$ and some "rough" geometric characteristics of the bodies like their diameter, then one would get the uniqueness in the general case by approximation. Such a stability estimate is claimed to be proved in Volkov's article reproduced as appendix to the new edition of Alexandrov's "Convex polyhedra", but the proof is flawed.