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[en] Besides the designed beam acceleration, the energy of electrons is changed by the longitudinal wakefields in a real free-electron laser (FEL) facility, which may degrade FEL performances from the theoretical expectation. In this paper, with the help of simulation codes, the wakefields induced beam energy loss in the sophisticated undulator section is calculated for Shanghai soft X-ray FEL, which is a two-stage seeded FEL test facility. While the 1st stage 44 nm FEL output is almost not affected by the wakefields, it is found that a beam energy loss about 0.8 MeV degrades the peak brightness of the 2nd stage 8.8 nm FEL by a factor of 1.6, which however can be compensated by a magnetic field fine tuning of each undulator segment. And the longitudinal coherence of the 8.8 nm FEL output illustrates a slight degradation, because of the beam energy curvatures induced by the wakefields.