I am cutting out segments from a long mp4 file and then rejoining parts of them. However, since FFMPEG apparently keeps the same MOOV atom for the trimmed files as the original, it looks to FFMPEG that the trimmed videos are all identical since they all have the same MOOV atom, and therefore only uses the first segment when trying to join the videos. Is there a way around this? Unfortunately since FFMPEG is embedded in an Android app, I can only use version 0.11.
Without knowing the exact details of your workflow it is hard to answer this question, so more information would be greatly helpful.
One approach would be to use raw video during your "joining" phase of the algo to strip the moov atom. The final step would be to convert your concat'ed raw video back into mp4.