We have studied the amplification of high harmonics generated by a short infrared pulse in a gas jet, injected in a free electron laser amplifier. The high-order harmonic spectra have been simulated using a 3D non-adiabatic model that includes both the single atom response and the effect of the propagation of the XUV field inside the gas jet. The response of a single atom to the IR field is calculated in the framework of the Strong Field Approximation (SFA); The nonlinear polarization associated to this process is evaluated as the acceleration of the nonlinear dipole moment. This term is used as source term in the propagation of the harmonic field inside the gas jet. The propagation effect are extremely relevant for the temporal structure of the XUV field as the coherent interference of the dipole emission of the different atoms leads to the selection of only one XUV pulse for each semi-cycle of the driving IR field. The amplification in the free electron laser has been simulated with GENESIS 1.3. The effects of filtering the seed spectrum have been analyzed and the coherence properties of the light are considered.