In the late stage of the evolution of a pion system in high-energy heavy-ion collisions when pions undergo multiple scatterings, the quantum transport of the interfering pair of identical pions plays an important role in determining the characteristics of the Hanbury-Brown-Twiss (HBT) interference. We study the quantum transport of the interfering pair using the path-integral method, in which the evolution of the bulk matter is described by relativistic hydrodynamics while the paths of the two interfering pions by test particles following the fluid positions and velocity fields. We investigate in addition the effects of secondary pion sources from particle decays, for nuclear collisions at AGS and RHIC energies. We find that quantum transport of the interfering pair leads to HBT radii close to those for the chemical freeze-out configuration. Particle decays however lead to HBT radii greater than those for the chemical freeze-out configuration. As a consequence, the combined effects give rise to HBT radii between those extracted from the chemical freeze-out configuration and the thermal freeze-out configuration. Proper quantum treatments of the interfering pairs in HBT calculations at the pion multiple scattering stage are important for our understanding of the characteristics of HBT interferometry in heavy-ion collisions.