Turbulent junction flow is a complex vortex system generated upstream of a blockage embedded in a turbulent boundary layer, which leads to augmented heat transfer in the vicinity of the blockage. The vortex legs wrap around the blockage and are carried downstream as longitudinal vortices. In scenarios such as multi-stage axial turbines or multiple row tube heat exchangers, these longitudinal vortices can collide with the next junction flow vortex on a downstream blockage. Furthermore, freestream turbulence is often present in these devices to augment mixing or increase heat transfer. This paper provides a comprehensive study on how a longitudinal vortex affects junction flow and associated heat transfer for a variety of Reynolds numbers, freestream turbulence values, and longitudinal vortex configurations. Longitudinal vortices were generated upstream of a Rood wing airfoil using a single, or pairs, of delta winglet vortex generators. Spatially-resolved endwall heat transfer coefficients upstream and around the Rood wing junction were measured using infrared thermography, and time-averaged flow field measurements of the incoming longitudinal vortex were taken using Stereo Particle Image Velocimetry. Longitudinal vortices provided some augmentation upstream and around the junction, but did not greatly increase heat transfer at the junction or disrupt the time-average horseshoe vortex. At high turbulence, longitudinal vortices were found to be less effective at augmenting heat transfer, with their effectiveness further decreasing at higher Reynolds number values. This was the result of decreased normalized vorticity at these conditions. Because of this, vorticity was determined to be a key parameter in determining quantitative heat transfer augmentation from a longitudinal vortex. Qualitative trends on the other hand are heavily influenced by the velocity vectors, as seen in how peaks in St augmentation were more narrow at higher turbulence levels. This was the result of secondary vorticity cores only present at low turbulence preventing fluid from being able to directly impinge on the endwall.