Recent clinical studies showed that the hemodynamic energy loss of the surgical conduit used in 3rd-stage repair of single-ventricle heart defects (Fontan surgery) determines the post-operative exercise capacity. Still, our understanding of the Fontan pathway energy loss is based on fully-functional conduits that are acquired from patients with optimal post-operative health, while a significant portion of the patients struggle with severe complications due to their gradually failing physiology. In this study, the hemodynamics of severely deformed surgical pathways due to torsional deformation and anastomosis offset, are investigated. We designed a mock-up circuit to replicate the mechanically failed inferior vena cava (IVC) anastomosis morphologies under physiological venous pressure (9, 12, 15 mmHg), in vitro, employing the commonly used conduit materials; PTFE, Dacron and porcine pericardium. For three twist angles (0°, 30°, 60°) and caval offsets (0Diameter, 0.5D and 1D) conduit shapes are digitized in 3D and employed in computational fluid dynamic simulations to determine the corresponding hydrodynamic efficiency levels. A total of 81 deformed configurations are analyzed in which the pressure drop values increased 80 to 1070 % with respect to the uniform diameter IVC conduit. Surgical materials resulted significant variations in terms of flow separation and energy loss. The porcine pericardium and PTFE conduit resulted 8 and 3 times more pressure drop than the Dacron conduit, respectively. If anastomosis twist and/or offset cannot be avoided due to the patients anatomy, alternative materials with high structural stiffness can be considered.