Amorphous, partially transesterified poly(ethylene terephthalate)/poly(ethylene naphthalate) (PET/PEN) blends of different levels of transesterification and blend composition were investigated in terms of resultant phase behavior, thermal transitions, and melt rheological properties. Intrinsic viscosities of the lowest transesterified material were found to be significantly below those of a physical blend of an identical composition, but at higher levels of transesterification, there was little difference. This was similarly found in melt rheometry measurements, where the zero-shear rate viscosity of the low and highly transesterified mixtures were similar. Both solution and melt rheometry indicated that the molecular weight decreased by thermal degradation from processing. This is believed to play an important role in determining the final molecular architecture and properties. For similar levels of ester interchange, there was a minimum observed in zero shear melt viscosity at around 40 wt % PEN. This is likely due to competition between the slightly transesterified copolymer chains having poorer packing in the melt and reduced entanglement. Differential scanning calorimetry and dynamic mechanical thermal analysis were used to investigate the phase behavior of partially and fully transesterified blends. Results for the glass transition of the highly transesterified blends were compared with the theoretical values calculated from the Fox equation and were found to be close, although slightly lower. A correlation between the melting temperature of the blend and the degree of transesterification was shown to exist. This correlation can be used to estimate the degree of ester exchange reaction from these melting transitions.