We consider a time-dependent atom interferometer based on splitting and merging an elongated Bose-Einstein condensate (BEC) along the weakly bound axis. The interference phase is imprinted at maximum splitting, and both arms are then recombined. We discuss a framework to include thermally populated low-energy excitations. Previous studies performed at zero temperature in the mean field description are extended using a truncated Wigner method. First results are discussed for the dipole mode oscillations in the recombined trapping potential.