A method of operating a selective deposition-based additive manufacturing system capable of building a three-dimensional (3D) part includes developing a first layer using at least one electrostatographic engine, conveying the first layer from the at least one EP engine to a transfusion assembly, determining an anticipated transfusion overlay error for the first layer, determining whether the anticipated transfusion overlay error exceeds an overlay error specification, discarding the first layer after determining that the anticipated transfusion overlay error exceeds the overlay error specification, developing a successive layer using the at least one electrostatographic engine, conveying the successive layer from the at least one electrostatographic engine to the transfusion assembly, and transfusing the successive layer on a part build surface using the transfusion assembly to build the 3D part in a layer-by-layer manner on a part build platform.