FLV Joining Tips
If the files you are joining have been encoded identically, then you should have no problem joining losslessly. However this is often not the case.
e.g. Sites like Youtube often encode each part slightly differently, which is really annoying! Your media player may say each part is the same, but the content might be encoded differently to the header. You can test this by joining the same part several times, if it plays back smoothly over the join then chances are the other part is encoded differently.
There can be plenty of reasons if you're having problems joining or playing back FLV content.
Success can depend on the codec your video is encoded in, either H263, VP6, or H264. I've found more problems joining h264 content than the other older codecs as the method to encode them is more variable. For playback, the program you use to play media can make a difference. e.g. VLC doesn't handle joined h264 content well, whereas MPC-HC does an excellent job.
There may also be broken or incomplete packets at the end of each file. It's never a good idea trying to join only partially downloaded clips.
• Update • I've re-thought my ideas on joining h264 flv files. If you can possibly do so, try Appending each part in AviDemux, select Copy audio and video and save the output as MP4. Test it and see if your favourite media player is happy with the joined result.
An example
I recently downloaded a multi part h264 video from Youtube, and while each part played fine there were problems playing the joined output. I suspected the audio was not encoded identically with each part, even though different media players said it was. This is absolutely essential to keep your media player happy. To fix it I used AVANTI (a front end for FFmpeg) and reprocessed using "copy" on video (lossless) and a set audio re-sample rate, and output as MP4 format. I then used AviDemux to join each MP4 file using it's append function. This works as long as the frame rate is not too variable - a bit "pot luck" as AviDemux can be unstable or otherwise work perfectly. You can try either app or a combo of each, obviously the output wrapper depends on the codecs used. My resultant MP4 file now played perfectly smoothly, and you can't tell where the join points are. Only the audio needed re-sampling (I choose the higher bitrate anyway) and the video is identical. I could have kept the FLV wrapper, but the MP4 wrapper is more compatible with standalone media players.
Hope these tips help, there's no such thing as a perfect "fix all" solution, so don't be afraid to experiment.
I wish you success joining your media.