ffmpeg -i recording.mp4 -c libx264 output.flv

ffmpeg -i output.flv -ss 00:00:00.000 -t 00:00:01.000 -c copy output2.mp4

Output file is empty, nothing was encoded (check -ss / -t / -frames parameters if used)

Duration: 00:00:26.96, start: 0.080000, bitrate: 126 kb/s
  Stream #0:0: Video: h264 (High), yuv420p, 640x480, 25 fps, 25 tbr, 1k tbn, 50 tbc

ffmpeg -ss 00:00:03.000 -t 00:00:01.000 -i output.flv -c copy output2.mp4