Recently a new method of controlling the pulse length of a short-pulse free-electron laser (FEL) has been developed. By modulating the synchronism between the optical and electron pulses in the FEL cavity, it was found that the output power and the micropulse length of the FEL beam oscillates at the modulation frequency. In this paper, we study theoretically the behavior of the micropulse length, both in the high loss (steady state) regime and the low loss (limit cycle) regime, when a modulated desynchronism is applied. In order to do this, we analyze the dynamics of a short-pulse FEL oscillator. The modulation frequency value plays an important role in the dynamics. We find that there is a resonantlike phenomenon between the externally applied desynchronism modulation and the limit cycle oscillation without modulation of a free-electron laser.