Since you do not mention format it is hard to give advice, but for mp4 this seems to be a good alternative. Even includes example of merging files.
Code taken from link:
MovieCreator mc = new MovieCreator();
Movie video = mc.build(Channels.newChannel(AppendExample.class.getResourceAsStream("/count-video.mp4")));
Movie audio = mc.build(Channels.newChannel(AppendExample.class.getResourceAsStream("/count-english-audio.mp4")));
List videoTracks = video.getTracks();
video.setTracks(new LinkedList());
List audioTracks = audio.getTracks();
for(Track videoTrack:videoTracks){
video.addTrack(new AppendTrack(videoTrack, videoTrack));
}
for(Track audioTrack:audioTracks){
video.addTrack(new AppendTrack(audioTrack, audioTrack));
}
IsoFile out = new DefaultMp4Builder().build(video);
FileOutputStream fos = new FileOutputStream(new File(String.format("output.mp4")));
out.getBox(fos.getChannel());
fos.close();
https://code.google.com/archive/p/mp4parser/wikis/AppendTracks.wiki
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