oftens just stripping container created during livestream, and then laying down video-audio streams to fresh made container fix these timestamp type things issue.
at least i say it have works for me somes of the times, may be you could trys doing it for your case to say the outcome?
by examples, use ffmpeg. this example is ms-dos command line, but yous could do linux command line if that is how you run ffmpeg.
Code:
ffmpeg -i "input.flv" -vcodec copy -acodec copy "output.flv"
where input.flv is you mess up livestream file, and output.flv is the re-fixed file.