How to cut and merge mp4 video segments without re-encoding?
Well, this doesn't solve the problem of the re-encoding, but at least it is an handy interface. Just use it (in Linux) with vcat -i inputfile1,inputfile2[start-end],... -o &lt;outputfile&gt; (it needs python3 and the moviepy package)

#!/usr/bin/python3

import sys, getopt, re

def printerror(errormsg):
  print("*** vcat - concatenate video segments using moviepy ***\n")
  print("ERROR:", errormsg,"\n")
  print("Usage: vcat -i inputfile1,inputfile2[start-end],... -o &lt;outputfile&gt;")
  print("Optional start and end points should be given in seconds. If files have spaces should be quoted (e.g. \"input file.mp4[5-30]\").")

try:
 from moviepy.editor import VideoFileClip, concatenate_videoclips
except ImportError:
 printerror("You don't seem to have moviepy installed. Install it with `pip install moviepy`.")
 exit(1)

def main(argv):
    inputfiles_arg = ''
    outputfile = ''
    try:
        opts, args = getopt.getopt(argv,"hi:o:",["input=","output="])
    except getopt.GetoptError as err:
        printerror(str(err))
        sys.exit(2)
    for opt, arg in opts:
        if opt == '-h':
            printerror("")
            sys.exit()
        elif opt in ("-i", "--input"):
            inputfiles_arg = arg
        elif opt in ("-o", "--output"):
            outputfile = arg
    if outputfile =='':
        printerror("Output file not specified")

    iFiles = inputfiles_arg.split(',')

    clips=[]
    for iFile in iFiles:
        subclip = re.search(r"\[([0-9\-\.]+)\]", iFile)
        if subclip is None:
            clips.append(VideoFileClip(iFile))
        else:
            dims = subclip.group(1).split('-')
            if len(dims) != 2:
                printerror("If a specific segment of a file is specified, this should be given as [startseconds-endseconds]")
            iFile = iFile.replace("["+subclip.group(1)+"]",'')
            clips.append(VideoFileClip(iFile).subclip(float(dims[0]),float(dims[1])))

    f = concatenate_videoclips(clips)
    f.write_videofile(outputfile)


if __name__ == "__main__":
   main(sys.argv[1:])


Disclaimer: I don't use Python by a while, so sure there could be better approaches.. bdw it's really nice to be able to do what you want to do in a few hours because of the enormous documentation you can find on the net about python..