Modeling and simulation for additive manufacturing (AM) are critical enablers for understanding process physics, conducting process planning and optimization, and streamlining qualification and certification. It is often the case that a suite of hierarchically linked (or coupled) simulation models is needed to achieve the above task, as the entirety of the complex physical phenomena relevant to the understanding of process-structure-property-performance relationships in the context of AM precludes the use of a single simulation framework. In this study using a Bayesian network approach, we address the important problem of conducting uncertainty quantification (UQ) analysis for multiple hierarchical models to establish process-microstructure relationships in laser powder bed fusion (LPBF) AM. More significantly, we present the framework to calibrate and analyze simulation models that have unmeasurable variables, which are quantities of interest predicted by an upstream model and necessary for the downstream model in the chain that are difficult or impossible to observe experimentally. We validate the framework using a case study on predicting the microstructure of binary nickel-niobium alloys processed using LPBF as a function of processing parameters. Our framework is shown to be able to predict segregation of niobium with up to 94.3% prediction accuracy in test data.