If you have two files, one with audio and one with video, you can use FFMPEG to merge them without re-encoding.
For this example, the video file will be video.mp4 and the audio will be audio.mp4.
To merge both files, you should use the following command:
ffmpeg -i video.mp4 -i audio.mp4 -c:v copy -c:a copy output.mp4
Once finished, the output.mp4 file will contain both audio and video together.